Shock can be repaired - see this thread:
http://217.199.188.40/xmb/viewthread.php?tid=15625 All the ss shocks should fit your bike. The later 900ss inj have the advantage of giving a higher ride height. They come up on ebay reasonably frequently. Monsters and 916/748 don't fit.
Put the bike on a rear stand and see if there's any side-to-side movement on the rear wheel. You should be able to get new bearings or at least order from any Ducati Dealer for around £10-£15.
Bob Hills may just be a decent dealer trying to give you a bit of warning about problems to come. Or not!
Hope this helps.