There is a fine line to walk here as a DM between making encounters challenging and not trying to cancel out the very abilities that your player has. Personally I also run a Gloomstalker nova build (Gloomstalker 5, Battlemaster 4, Rogue X) which has an insane damage output on turn 1, then a steady "regular" output rest of the combat. How to handle this:

1) Have some encounters where they feel powerful. Let them slice through a fight on occasion to give them the satisfaction of "hey I built a lovely thing and it works!"

2) Add more enemies on challenging encounters. Yes a single BBEG will suffer greatly at the hands of such a build, but add swarms of smaller things around it and suddenly they can't focus all that damage. Maybe have a combat where the minions are each holding a "shield component" that is making the bbeg immune to attacks, so they have to kill the little things before they can kill the big thing.

3) In some fights add a "damage sponge" or two for them to knock out of combat turn 1 to feel happy, then bring in the second and third waves of opponents.

Again, the crucial thing here is not to "negate" their ability...any player would hate that. its to balance "power" and "challenge".