I'll start by saying that I've tested these concerns using versions 2.5.0.168 and 2.5.1.184. In the former case, I was using the recommended release of Forestry, while the latter release would not load until I updated Forestry to a more-recent beta release, 5.8.2.372. These concerns were present in both.

Things that seem to be bugs:

1. Acclimatiser consumes buckets along with their contents. This is true of both water and lava buckets. I suggest that unstackable items (at the absolute least, buckets) should turn into their container items (if a container exists), rather than be destroyed outright.
2. When an acclimatiser successfully makes a change to a queen, that queen is restored to full health. This is definitely not appropriate, and could theoretically be exploited to keep a single queen alive for much, much longer than her natural lifespan. I suggest taking a look at the NBT-reading/writing methods and look for a system that is default-inclusive, rather than default-exclusive, as I suspect it currently is. EDIT: This also resets the generational age of ignoble princesses and queens to zero.
3. There does not appear to be any visible progress indicator on the GUI. The only reason I think this is a bug is because a tooltip appears when I hover over the globe icon in the background. It can be a bit difficult for me to know if the machine is working.

Feature requests:

1. The acclimatiser cannot use several vanilla items that would seem like logical acclimatizing items. Examples include snow blocks, snow layer blocks, packed ice, water bottles, and wet sponges. I suspect that the system has the same chance of success regardless of the item being used, which would explain why some of these items may have been deliberately excluded from the list. If that's true, this functionality would need to be added, but I suggest that these items be added to the list of viable input items.
2. The block is called an "Acclimatiser," but it's tooltip expressly calls it an "Acclimatizer," with a Z. As the world acclimatize is also spelled with a Z (at least in my part of the world), I'd suggest maybe the name of the block be changed to have a Z as well? At the least, I think the spellings should match.
3. There seems to be no in-game indicator for what items are acclimatizing items. I'd suggest that this information be added to one of the in-GUI tooltips, as part of NEI integration, or both.

Can confirm this behavior is still happening in 1.12.2-2.5.1.186. Also, the acclimatiser does not accept IC2 universal fluid cells, which would be most convenient since it seems to take a massive amount of water to shift humidity tolerance.