Of course, those banks that hold excess reserves face a direct cost from the negative deposit rate. In addition, to the extent that banks cannot pass through the lower rate to all types of depositors, the net interest margin of banks is also compromised if competitive pressures mean that lending rates fall by more than deposit rates.
That said, in the other direction, banks benefit from lower wholesale funding costs and the improved ability of customers and sovereigns to service existing debts, while also booking capital gains on holdings of fixed-income securities.