For the collector I could see it being a dealbreaker, but for someone who actually plays the instrument it shouldn't matter. Heck, Fender even makes the same/similar vintage style cases currently in black telex, brown telex and even tweed, so if you're into keeping the same look you can buy those cases for under $150.
If you're someone who's into having everything original on a bass, getting all the original case candy, original case, etc., you're better off just buying new. But with that said, don't buy "new" from Guitar Center unless you watch them take it out of the original shipping box, because they are notorious for raiding cases of the case candy! I've even had them try and tell me that the guitar I was interested in didn't come with a case or gig bag, even when I pulled the guitar up on the Fender site and it clearly stated "comes with hardshell case"!
I went through a Jazz bass search last year and came across a guy selling an American Professional Jazz for $650! Only thing was he installed pickup and bridge covers, but screwed up the bridge cover the first time, so there were two sets of holes, hence the low price. I bought it, but didnt bond with it, so I sold it for what I got it for minus the case and kept that really nice Fender American Professional case for my Classic 70's Jazz.