Achievements in Hydra are unlocked based on certain files that register the achievements.

Hydra maps and interprets these achievement files, so whether or not achievements work depends entirely on the games themselves, and whether they are generating and recording unlocked achievements in a file.

If your achievements in a certain game are not unlocking, it is not recording achievements, so there is no way for Hydra to unlock them. Now, if they are, they will unlock normally!