If I update to Kontakt 8 now for $99, will it still cost me $399 to update to Komplete Ultimate in the future? ((a month or so from now)
Yes.
Upgrading Kontakt has no bearing on updating/upgrading Komplete.
And remember - the NI store will take your money regardless of what choose out there. But you should watch for duplication at all times.
I am guessing you probably do not want to pay twice for the duplicate copy of Kontakt you will end up with.
If a user owns Komplete - best value (but not necessarily what is best for your wallet :) - is to always consider updating Komplete when possible.
In your case - the Ultimate to Ultimate (Update)
VP
Thanks for confirming.