Here's a question - why are dragon's respawning? Sounds like the glitch isn't that the re-spawned dragons don't have souls, but that a dragon whose soul you absorbed can re-spawn at all. I remember one of the characters in the game saying the the dragon born has the power to permanently kill a dragon, because they absorb the soul, so the dragon can never resurrect again. So, if a dragon whose soul you absorb resurrects (re-spawns), that sort of violates the whole idea of you being the only person able to permanently kill a dragon.
The only problem I might see arising from that is, let's say there's a word-wall dragon that you went and killed while getting a word. Then, you go to town and their's a bounty/quest to kill that dragon - if the quest isn't smart enough to realize you've already killed it, and let you immediately claim the reward, then maybe you could be stuck with broken quests that can never be finished. That would be bad.
I'm not an expert, but I understand there are Named, quest related dragons and non-named generic dragons. To address your second question first, I think the game would treat them like any named NPC and track them. Of course, since quest related NPCs in Skyrim appear to be Essential and therefore unkillable (unlike OB) it's hard to make a judgement about the dragons.
As for the generic dragons it's a glitch one way or the other; either they respawn without souls or they never had a soul in the first place.