I think it's a shame to remove them entirely but they could certainly be moved elsewhere or used in a different way if you wanted to have somebody different in those levels.
For this I have some ideas.
If this is not the true Hydra base, then perhaps Hammer and Bowman can be at the real one instead (it makes sense that they would not all be at the same one) and be a double boss fight. By that point in the game, having two bosses instead of one would be an appropriate level of challenge

Although they would definitely need toning down in either health and/or AI because Bowman still feels ridiculously hard to hit and avoid so he could use a little nerfing anyway, and Hammer, while easier, is still a horrid fight for some characters (such as Hawkeye and Widow) so having to fight both of them in their current state would be rage inducing, lol.
Alternatively, to give the fight a unique mechanic without having to fight two bosses at once, you could have it so that one of them is out of reach. Bowman could be shooting arrows from a vantage point whilst you fight Hammer down bellow (Bowman should still be visible for cinematic purpose), and once you defeat Hammer, his hammer could fly out of his hand and knock out Bowman to explain why the fight ends by killing Hammer. Or perhaps Bowman could leap down from his vantage point and you have to fight him. So rather than two bosses at once, you fight one after another, with the second one helping a little in the first battle.
Personally I think this idea could be pretty epic looking in action

I'm envisioning Bowman targeting similar to the sniper-type things we have in other levels and you see him with the arrow drawn and then he fires at whatever spot he aimed at, so you constantly have to dodge him and keep an eye on where's aiming. Perhaps he could occasionally fire special arrows too or perform other actions (such as call minions) depending on how elaborate or difficult you wanted it to be

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What do you think?