As far as Suder was concerned, Janeway's goal wasn't to simply keep punishing him for the next 70+ years but to bring him back to a point where he might be useful to the ship and crew. That included radical "mind-meld" therapy and allowing him some measure of normality, as would befit someone who had committed a crime from a position of mental illness.
JANEWAY: I don't. I prefer to rehabilitate him, not to end his life. We'll confine him to quarters. Work with Kim to install maximum
TUVOK: Pardon me, Captain, but allowing him the comfort of his own quarters doesn't seem an appropriate punishment for murder.
JANEWAY: If we don't get home soon, he'll be in that room a long time, Mister Tuvok. I think this is the best we can do under these
By comparison, Paris' punishment is exactly that, intended to actually punish him. By depriving him of the most basic facilities, Janeway seems convinced that he might actually learn something from his transgressions, in the same way that he was improved by his time in the prison on New Zealand.
JANEWAY: I admire your principles, Tom, but I can't ignore what you've done. I hereby reduce you to the rank of Ensign, and I sentence
you to thirty days solitary confinement. Take Ensign Paris to the
PARIS: I know the way.
Purely as an aside, you may wish to note that it's pretty normal (in most countries) for long-term prisoners to be granted better facilities than those serving short-term sentences.