That's sounds high.
Neptune typically starts out with her swordplay and CQC, since that's mainly how she fights. She does have a few ranged moves, namely her Type 32 EX Blades as well as some energy attacks that she can use from afar, but in terms of what she's opening up with, CQC is her main choice.
EXE doesn't mess around, if he sees his normal attacks aren't doing much he'll break out the hax in short order. He can terraform the battlefield to reduce the damage he takes too.
EXE usually fights at a distance as his general MO
The speed amp is an issue, but EXE can use gravity manip and black holes to hold Nep in place and his LS is greater than hers. Also could terraform the battlefield to suit him better such as with Area Steal so she can't even get closer to him, I know she can teleport but EXE doing this will be something she has to address while he can formulate a plan in response. Plus he can throw up barriers and a defensive aura to protect himself. For starting moves EXE likely opens with shooting or anything else really afaik.
By the time he'd be seeing that his normal attacks do nothing, Neptune would have had plenty of time to smack .EXE with an attack. I dunno if he starts with any one of his hax in-character, but assuming he doesn't (you'll have to clarify on that one), then .EXE will simply be crippled before he gets a chance to counterattack.
That doesn't really matter that much since Neptune will also be inflicting him with the status effects that come with her attacks. Same can be said for Neptune's as well; her damage reduction won't matter much if .EXE just busts out the hax right away.
The OP clarified that the starting distance is 20 meters (how the hell is that even possible in a location like a hospital room???), so his ranged attacks aren't necessarily going to matter here, since Neptune can just easily close the distance given the speed gap.
Considering you yourself say that .EXE's starting move would (likely) involve shooting:
I'm not really inclined to believe that he's going to open up with something like a black hole, especially given the location that the OP has set the fight in (which sucks ass, don't get me wrong, but it is what it is). If he does indeed just begin with shooting, then Neptune can not only easily dodge it, but it just gives her enough time to close the distance and smack .EXE with an attack to cripple him.
Just based on the description provided for Giga Freeze in the NA&T part of .EXE's page, it doesn't even look like it's Sealing, just that it freezes someone in place for an indefinite amount of time, which is something that Neptune resists, given she resists the spatial-temporal freezing effects of the Trendi Phenomenon.
This is fair, though how is it activated? Is it an AoE kind of ability, or is it something .EXE has to hit Neptune dead-on with?
The hospital room is made for giants.
The homing attack doesn't even seem to have any justification attached to it. Not that it matters, Neptune has dealt with homing attacks before through things like Uni's homing bullet attacks, so they're not something new to her; she can still outpace it since she's faster.
She's been able to deal with six enemies at once, all by her lonesome, of which, she's dealt with six mechanical replicas of herself and her fellow Goddesses, which all have the same level of skill as the real deals and thensome. .EXE duplicating himself isn't gonna be an issue, either.
By vitality, do you mean life force or something similar? Because if so, she resists Life Force Absorption from Zaikopath, so if that is what you mean by vitality, it won't really work. Even then, her life force is the equivalent of a Type 1 Abstract that .EXE hasn't shown to have the feats to interact with, so draining her life force would be off the table regardless of if she resisted it or not.
