As the man page for bwa states, X0 is meant to report the number of best hits ... not just any old hit.

I believe this number is easier to interpret on a single read basis (ie, not for paired end reads or a "read fragment").

I'm not sure what you mean by "the number of unique locations aligned" -- because if there is a unique location, then the value of X0 would always be 1, right?

Anyway, this is the way in which I understand it (and this is only reads mapped with samse):

If two different deletions in your read cause it to align to the same place, I suspect that bwa would not call it as aligning to two different places, ie. the value of X0 would not be incremented. If, however, a single deletion aligns the read uniquely to chr 1000 and separate deletion elsewhere in the read would align it to chr12 1000, assuming these are the best alignments (ie. there is no perfect alignment to somewhere else), then the value of X0 in this case would be 2.

Of course Heng is the best person to answer. He sometimes haunts these forums, so hopefully he will clarify any misunderstanding we may have.