Regarding no-supply-degradation, I think that could be highly undesirable in practice, because it would emphasize timing to a really great degree. It would also lead to situations where you could get your fleet to some planet, and then there would be no way to bring that same fleet home (hmm, that part actually sounds pretty good).
I suppose that would make more sense if transports automatically regened in planets where there WAS supply, and automatically lost health everywhere else. Really, the way that I am using transports right now is based on them losing health based on random enemies that the various planets, so it would be much the same thing. To keep things simpler, possibly transports should then be invincible to normal attacks, and then have that sort of degradation-over-time.
Of course, "time" is a rather variable thing, too. That will vary based on relative wormhole positions at each planet, and based on the attention of the player in some cases. Possibly it would be better to just have "going through a wormhole into a non-supplied planet" cost (for instance) 1/5th of the max health of the transport. That way you can make a total trip of 6 planets into enemy territory, or a round-trip of of 3 planets out and back. But conversely, if you sent these along a path that included planets of your own on every 6ish hops, then you could send these very far indeed, which is also desirable. Perhaps making it so that these heal superfast (as in 30ish seconds to completely heal from 1hp) when in supply would be good along with this.
Thinking about this more, that last paragraph is probably my preferred solution at the moment. It's just a twist of the "time" based one, without making players rush.