The amounts under "unallocated items and discrepancies" include the statistical discrepancies between the two systems of accounts. The assets of the central bank and the liabilities of banks exclude foreign currency swaps. The assets and liabilities of banks exclude the components matched by domestic foreign currency positions, which are included directly in the figures for the State and private sectors.
The answer is that the alternatives to depositing excess reserves are also costly. In fact, the cost of using alternatives to central bank deposits determines to what extent the rate on excess reserves can go negative in practice. Banks can always choose to hold physical currency instead of electronic money in their accounts with the ECB.