I am not aware of any that does. With modern hardware, and in a personal finance context (a few transactions per day), it is unlikely you will have too much data to handle. The algorithm to compute a balance is O(n) with the number of transactions, or O(nlogn) if the tool allows for unsorted input.

If required, you could always close a balance in one file and start with new accounts in a new file, sharding your journal by year, for example.