This issue is confirmed with irssi-fish from repository https://download.opensuse.org/repositories/home:/ailin_nemui:/irssi-git-an/xUbuntu_22.04/amd64/ and possibly other FiSH plug-ins
Despite fish encryption/decryption working while the FiSH module is loaded in Irssi, trigger.pl does not currently read FiSH decrypted messages in channel. For example, consider the following message in #irssi on Libera:
> This is a FiSH decrypted message
trigger.pl sees this message in its encrypted format which looks something like this:
+OK YRAtW0aJTWs0FV2ij/pXiSp/X0..k.95Izl1FwABA/LJ0x60
So unless the trigger is set to some variation of the above string, the trigger will never work.