Let me preface this by saying you should always be playing Nova vs. most HM teams even if it’s with one of his bad matchups up front (Dante, Wolverine, Spencer and Hulk to some degree). Viper has her way of fighting flood teams but Vajra tends to get bopped pretty bad by Missiles, and the Nemesis team is garglemesh anyway, thus the Nova team has better overall options to deal with it. (I also can’t really give you good Viper advice lol)
I personally don’t have a problem with missiles unless they’re being protected by Soul Fists, Dark Spells, or a big body. Nova has ways to maneuver around them in neutral and good ways to punish them once they get lazy with their calls. Don’t be afraid to hyper punish them with Gravimetric Blaster or Speed Tackle. If they’re smart they’ll stop calling it so brazenly and if they’re dumb, they’ll keep calling it and lose their Doom. But more importantly, you have access to Plasma Beam which is the scissors to Hidden Missiles’ paper. It depends on your opponent’s options, but unless they have a way to snipe your Doom, you can just call it when you hear them call theirs and it’ll blow through basically everything to hit Doom. Bolts is good for this too, but it’s pretty slow and leaves him quite vulnerable, so I don’t think you can call it with quite the same impunity as Plasma Beam.
I also want to emphasize patience. Nova doesn’t always have to go in; chilling in the upper corner with a shield in front of you is a fine way to wait out the missiles and put you in the best situation to call your Beam in reaction. Even Morridooms and Doomammus (lol) get impatient sometimes, and you might see them move forward to try and stop you from playing this way.
If you really feel like “this guy is ass and it’s only Hidden Missiles making this match hard,” then snap Doom in every time. Do it mid-combo, do it in reaction to slow normals or air grab attempts, do it when missiles are about to cockblock you as TenguEgg said. In the end you have to take care of what gives you trouble and not play into your opponent’s structuring.
Lastly, keep in mind that while most players online are dummies and it might seem like HM is their crutch, there are also a lot of players online who are smarter than they seem and are using the assist to their advantage. I know this doesn’t seem like much for consolation, but don’t beat yourself up too bad. But if their active Doom is also bad, idk anymore. Good luck to you.
PS: If you’re on XBL I can run a Hulk/HM team against you sometime to give you practice.