Don't make it JUST about Perception
Perception is a useful skill, Many games (Pathfinder esp) made Perception the king of skills that creates live-or-die situations based on such checks.
As was stated by others: do not nerf the player for building his character as a Perception-Monkey. He SHOULD get benefits from it. But that does not mean he should always benefit from it.
Personally I do three things to go around this: change the situation with conditions, encourage the use of OTHER skills, and have the "surprise round" be the creatures revealing themselves.
Change the situation: Use fog/ smoke, complete cover/ line of sight. At level 20, the PCs should not be fighting basic goblins or orcs. They are taking on world-spanning horrors and dangers. So most of their enemies will vary their tactics. Since the PCs are level 20, their enemies will have access to some of these high-levels spells that allow them to hide or distort reality, heck they might even teleport or plane shift in!
If the PCs keep running into the same situation where Perception is king, then yes, there is very little you can do.
Use of other skills (all of which I've seen used with Perception)
You look for tracks: That's Survival
How was the guy killed? That's Medicine
You look for a book in the library: That's Investigation
Find if that gambler has a tell: That's Insight
Finally, by having a reveal as a surprise round, you give the PC their bonus. I hate when my GM drops a surprise round with an initiative-monster so you take 2 monster attacks before you can do anything (that may have been worse in other edition, but the distaste still remains). So I do not write surprises in my stuff anymore. Or I do so very rarely.
Part of this, I will have reinforcements arrive from another location. The PCs engage the orcs from the front, well two rounds later, another band appears from the side. I tell the PCs "you hear noises coming from here," and let them decide if the concentrate or ignore the side group.
The trick is to change things without negating their ability. Changing things up will challenge them in more ways then one.