Basically, no.
I'm guessing that what you want to do is make some annotations that would tell the JPA to create additional indexes when the JPA system is used to create domain tables.
Otherwise, JPA is basically design against an SQL database, rather than being DB agnostic (I suppose someone could create a JPA implementation upon a pure ISAM model, but it would be a lot of work, and would effectively be writing a SQL database).
I, personally, don't know of any SQL database that allows maintenance of indexes to be optional. I've only seen that when working with ISAM databases (where in many cases, the programmer was responsible for maintaining all of the indexes himself).
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