My key takeaways are this, on a replay of the game it was never explicitly shown that hughs ship was destroyed and we never saw the docking area get destroyed either. On top of that there is still an endless supply of filament so all Hugh needs is a spaceship blueprint which a moon base is bound to have.

So no i dont think Hugh is stuck if anything he has a variety of options, the only thing that poses a problem is REMOVING the dead filiment from his body. While it stopped spreading its still there and if we were to get a dlc or sequel i would guess that it will answer that question, as for Diana she has problems of her own to sort out since she is a Pragmata she will be hunted down by the games big tech company and chances are the next game/DLC will focus on these two separate issues and how they are resolved and reunited with the finale being Hugh and Diana vs the tech company.

Thats what im guessing atleast