Having multiple bank accounts isn't usually a thing to avoid negative interests in Germany. It's that payments between banks took three days to settle (I think they're down to 1 day now), while payments between accounts at the same bank usually settled immediately. It's much easier to have multiple accounts with the largest banks so most of your customers can use bank-internal transfers.

Also, it's usually a good idea to have a backup just in case something goes wrong with your primary bank account. Dealing with bureaucracy is bad enough, dealing with it while you're also unable to send or receive payments is way worse.