There are really two issues at play here: detecting which of your indexes are under-used, and detecting which indexes are absolutely not used. The first is a matter of profiling, monitoring, logging from your own side, and the second is a matter of running
appcfg.py vacuum_indexes to delete any indexes which aren't explicitly mentioned in index.yaml (that is, any indexes which you didn't explicitly code for).
You could make a Feature Request in the
Public Issue Tracker for something which could help with this, such as collection of statistics in the Developers Console as to how often an index gets hit in a given time period.