I always dislike it when DM's try to counter specific abilities unless it's an intelligent opponent who knew to spy on the party. As a DM I always just decide general themes for areas, and of course some things might be more useful in those areas than not. Me actively going "well, they're in the underdark that's supposed to be infested by undead, but we have a cleric and a paladin so that seems really easy. Now it's all just illithid" feels like. So mean. Let them use their class feature, if they end up steamrolling the area then like, that makes sense? Thematically a cleric rolling up to a lichs castle and making the fight WAY easier cause they nuke all the zombies makes sense. Of course there's still challenge, the lich is difficult, but like, that's kinda the point of Cleric's ability.

When this happened my players didn't have less fun, they just all gave the cleric and the paladin way too much praise for about three weeks of play, and for that arc they were the MVP's. There were constructs and elementals, but mostly undead, and they made those fights much more tolerable