Denying the rogue a place to hide is not a solution.
Would it be OK to make it difficult to get into, or stay in, the places to hide?
I think we've all seen a movie where the hero detects enemies approaching. The hero looks around and there's no hiding place! The enemies come around the corner, and the hallway is strangely empty, and they just walk on by. Then the camera pans up, and the hero is
on the ceiling, holding themselves aloft by pressing hands and feet against opposite walls. (Presumably some kind of Athletics or Acrobatics check -- not that I want to restart that tired old debate.)
OR the classic: the hero is in a maze of shipping containers down by the docks. Enemies with submachine guns are searching for him or her. But the hero picks them off one by one! (The challenge here is for the rogue to detect the enemies using Perception; if they fail to do so, the enemy comes around a corner and just spots them.)
OR how about: The hero needs to cross open ground, with scant cover. Can they dive and roll behind various crates and barrels? Wait until the guards' backs are turned or the spotlight is pointed elsewhere? Time their movement to coincide with a passing cart or passing shadow? (Even if you consider these tasks to be Stealth-based, depending on the circumstances the DC might be incredibly high. Like, an ordinary person might have
no chance of hiding behind a tree that narrow, but our ninja PC can hit the required DC 30... usually.)
OR the hero can create a distraction! (Possibly some kind of Deception or Sleight-of-Hand trick to make the guards actually abandon their post and check out that sound.) How about some teamwork -- another character distracts the guards so that the hero can slip in behind them!
OR difficult terrain can be an issue. Maybe the only way to stay behind cover involves a difficult jump, a walk along a balance beam, or squeezing through a hole? (Athletics, Acrobatics, maybe thieves' tools if a door is locked.)
OR what if some other thing is making sound? The stolen MacGuffin might be noisy and clanky, or be an incompetent NPC. We know the hero can sneak up behind that guard, but can he or she kill the guard silently? What if the guard tries to shout? (Maybe you use grappling rules for this. Maybe slitting a throat silently is more Sleight of Hand than Stealth.
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Now, if all you are talking about is combat, then it's fine for the rogue to hide every single round and get Sneak Attack every round. That's kind of by design. In some environments the enemies can move to flank and get line-of-sight on the rogue, but usually the PC can just Cunning Action Dash their way into a better hiding spot.
The only tricky issue here is Blindsight, and whether or not mundane Stealth skill works on it. Generally you can't Hide from someone who can "see" you unless you are "obscured," so I think it's fair to rule that a creature which "sees" by hearing, temperature, vibrations, scent, etc. isn't going to be fooled by shadows, foliage, a conveniently-placed barrel, etc. The bigger question is, what counts as "obscurement" to Blindsight? Can Blindsight see right through solid objects? A wall may block light but not sound, for example. (Recall the scenes depicting
Daredevil's senses in season 1 of that show, where he can pinpoint people blocks away.) Would white noise block sound-based Blindsight? Would wind block scent-based Blindsight? Would soft, absorbent clothing block Echolocation? How does ooze Blindsight even work? I have no answers, but I can tell you from experience that every time the rogue gets spotted by Blindsight, that their player is going to be asking these questions.