Seizing a domain name is not a big deal, any domain, for that matter. But seizing domains that don't officially sit in the US jurisdiction will be another violation of sovereignty (as far as I understand it). And while technically it might not be difficult, it could be next to impossible politically. What prevents Bitfinex from registering a new domain in some US-hostile country, say, Iran? As I see it, domain names should be Bitfinex' least concern.
Seizing the domain is about making a statement. The banking world would shut them out (well, already done in Bitfinex's case), and they would forever have a target on their back and risk of seizures.
Further, Bitfinex is a whole lot larger than Btc-e, and they had tensions with the CFTC in the past, so, first, they are more tasty than Btc-e, so to speak, and, second, they should be prepared to the US "law enforcing" agencies to go after their servers (and even more so now that Btc-e servers got seized). So the real question is whether the US already tried that but failed or they are yet to try. Besides, Bitfinex has already been blacklisted by the US banks (see Wells Fargo), so there likely was (is) something going on behind the scenes, and it kinda looks that this exchange is far better prepared to the kind of attack that Btc-e fell victim to
I think it's more just a matter of time. The feds take years to build these cases.