I don't see where it really adds much value to keep these hulks floating about. If you want to introduce something navigational, you could consider including a debris template of some sort that persists during the fight -- an interesting idea, actually, in the case of extreme explosions (hmm) -- but drifting ships of speeds that we need to track of because of the persistence of critical effects sounds like a lot of overhead and number-tracking for something that most players just take off the darn board anyways.
Drifting ships should only be left on the board in one case -- no crew, damage points still remaining. This may be relevant in campaigns; as owners may be able to retreive some functional ghost ships (as pointed out, I see, in retrospect, by Mr. McGhee). But that's about it.
As to bigger explosions ... that feels like a problem. You would be tempting several fleets to base entire tactics on this if it gets out of hand; combine this with the massive squadrons currently permitted for some crazy reason and you could go crit-trawling on a massive scale. It wouldn't be too difficult for some races to get to the ludicrous damage necessary -- sets of Saggis (broadside with Flash or Heavies), the Solarhawk (on "hot" turns), and the Rohric (if Mass Drivers on speculative fire are able to connect) are fairly cheap ships that can, at ranges of 10" plus, easily create 20+ points of damage against lightly-hulled ships. The Shantavi is a more expensive option. This would already only serve to further promote the problematic I-Fire-You-Fire-What's-Left phenomenon that we are already heading towards with these unfortunate 6-squadron Armageddon rule. That's a Warhammer phenomenon that I can well do without.