Tl;dr: Based on the pictures of the boards, the only Z490 Mini-ITX board definitely compatible with NH-C14S in either orientation is Gigabyte Z490I Aorus Ultra. ASRock Z490M-ITX/ac possibly is. Others seem to be only compatible in the orientation where the heatpipes are towards the PCIE slot. Is there anybody who could confirm?
Now that the first Intel 10th Gen Mini-ITX boards, namely the ones with the Z490 chipset, are out, I thought to check for the compatibility with the NH-C14S. (I'll probably eventually build a rig with those, but not before the next RTX 30x0 cards are out.) A huge cooler with a huge fan, but can still fit e.g. a Streacom DA2 or Ncase M1 (with the cooler below the heatsink).
Even with the Z390 boards there was a problem with the huge VRM heatsinks these motherboards started boasting, with big shrouds enclosing the whole IO shield area. I didn't own any, but I don't think any one of those could fit the C14S in the preferred orientation (in the Streacom DA2, the only orientation where you can fit it below the top dust filter), that is, the heatpipes towards back of the board (the IO shield side). The ASRock's non-Phantom board perhaps was the only board fully compatible, as it didn't have that kind of shroud.
With the new Z490 boards the situation hasn't changed much. The heatsinks with their shrouds are still huge, height as much as the IO shield and width of about 42 mm. But at that point below the C14S's heatpipes there's only 33 mm of room. Noctua lists all those boards as "fully compatible", but I don't trust them. Noctua only makes their compatibility reviews based on estimation from the motherboard pictures and only try borderline cases with actual physical boards. I believe with these, just as with Z390 boards, they've either inaccurately estimated the Z dimension requirements with the heatpipes, or just list the boards as fully compatible, if the cooler can fit in at least one orientation (the one where the heatpipes are towards the PCIE slot; however, with ever enlarging M.2 heatsinks, you can't be sure of that either).
Hopefully the picture below illustrates the problem. This one is with Asus ROG Strix Z490-I Gaming and this preferred orientation. MSI's MEG Z490I Unify and ASRock's Z490 Phantom Gaming-ITX/TB3 seem to suffer from this problem as well.
However, the positive surprise is the Gigabyte board (image below). This time they've gone with an efficient VRM cooling solution, it seems. While others go with active cooling, which doesn't seem to help anything (According to Optimum Tech), Gigabyte's VRM cooling seems to be both small, passive (i.e. not contributing to any noise) and cooling just as well. Based on the images of the board, I'd say the cooler will easily fit in both orientations. In the other orientation, it's not as clear a case, but based on the pictures I'd say that the M.2 heatsink height is below the 33 mm limit.
Even ASRock's Z490M-ITX/ac board (image below) now has a big heatsink. That one isn't a clear case as the VRM heatsink is sloped. It's really hard to accurately estimate its height at the lower end of the slope, so that one is a definite "maybe". The slope may be at the required 33 mm height, but it's so close that only with pictures I wouldn't trust my estimate would be accurate enough. [Edit: The heatpipes do clear, but the offset of the whole socket towards the top may pose a problem with the top of the case. See more in the comments below.]
If somebody happens to already own one of these boards and a NH-C14S cooler, could you confirm my estimates? I already emailed Noctua's support with my question as well.
And naturally, this is just based on the boards au naturel. If you just strip off the VRM heatsink and make your own custom cooling solution, this doesn't matter.
Now that the first Intel 10th Gen Mini-ITX boards, namely the ones with the Z490 chipset, are out, I thought to check for the compatibility with the NH-C14S. (I'll probably eventually build a rig with those, but not before the next RTX 30x0 cards are out.) A huge cooler with a huge fan, but can still fit e.g. a Streacom DA2 or Ncase M1 (with the cooler below the heatsink).
Even with the Z390 boards there was a problem with the huge VRM heatsinks these motherboards started boasting, with big shrouds enclosing the whole IO shield area. I didn't own any, but I don't think any one of those could fit the C14S in the preferred orientation (in the Streacom DA2, the only orientation where you can fit it below the top dust filter), that is, the heatpipes towards back of the board (the IO shield side). The ASRock's non-Phantom board perhaps was the only board fully compatible, as it didn't have that kind of shroud.
With the new Z490 boards the situation hasn't changed much. The heatsinks with their shrouds are still huge, height as much as the IO shield and width of about 42 mm. But at that point below the C14S's heatpipes there's only 33 mm of room. Noctua lists all those boards as "fully compatible", but I don't trust them. Noctua only makes their compatibility reviews based on estimation from the motherboard pictures and only try borderline cases with actual physical boards. I believe with these, just as with Z390 boards, they've either inaccurately estimated the Z dimension requirements with the heatpipes, or just list the boards as fully compatible, if the cooler can fit in at least one orientation (the one where the heatpipes are towards the PCIE slot; however, with ever enlarging M.2 heatsinks, you can't be sure of that either).
Hopefully the picture below illustrates the problem. This one is with Asus ROG Strix Z490-I Gaming and this preferred orientation. MSI's MEG Z490I Unify and ASRock's Z490 Phantom Gaming-ITX/TB3 seem to suffer from this problem as well.

However, the positive surprise is the Gigabyte board (image below). This time they've gone with an efficient VRM cooling solution, it seems. While others go with active cooling, which doesn't seem to help anything (According to Optimum Tech), Gigabyte's VRM cooling seems to be both small, passive (i.e. not contributing to any noise) and cooling just as well. Based on the images of the board, I'd say the cooler will easily fit in both orientations. In the other orientation, it's not as clear a case, but based on the pictures I'd say that the M.2 heatsink height is below the 33 mm limit.

Even ASRock's Z490M-ITX/ac board (image below) now has a big heatsink. That one isn't a clear case as the VRM heatsink is sloped. It's really hard to accurately estimate its height at the lower end of the slope, so that one is a definite "maybe". The slope may be at the required 33 mm height, but it's so close that only with pictures I wouldn't trust my estimate would be accurate enough. [Edit: The heatpipes do clear, but the offset of the whole socket towards the top may pose a problem with the top of the case. See more in the comments below.]

If somebody happens to already own one of these boards and a NH-C14S cooler, could you confirm my estimates? I already emailed Noctua's support with my question as well.
And naturally, this is just based on the boards au naturel. If you just strip off the VRM heatsink and make your own custom cooling solution, this doesn't matter.
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