We don't really know what's happening when it comes to intel in the game - the devs simply haven't explained it to us, other than "it's similar to BOTF but with more options".
As for Stellar Phenomena like Nebulae, these are gonna be huuuge in the game, possibly taking up multiple sectors. (If sectors are in, of course)
I don't know if "deadly Nebulae" (:lol:) could be programmed in, or whether it would be desirable from a programming point of view - if crew are killed off, then your ships are gonna need a crew counter, and it'll be just another stat that the game - and the player - will need to keep track of.
For more experienced players, this would be a good idea, but from the point of view of newbies, it would be even more confusing. This game isn't just aimed at the fans; it's also aimed at those who don't know that they like Trek games yet.
I know what Nebulas you mean though, i've got Armada 1 and still play it. Did you know that the green Nebulas recharge your shields and special energy?
Anyways, as i've said to many people before, the only way you'll get the answers you want, is direct from the devs themselves.