In addition to GrandFathers good questions, also consider how the query requirements will change. If you envision only a limited set of queries it might be convenient to keep the data in a Perl data structure. The limited set would be restricted to simple counts all things, or hierarchical counts of things that fit within the hierarchy of your data structure.

If you can think of nifty reports on things in your data, or don't even know what other things might be interesting to report on, SQL is far more expressive than Perl for writing reports, at least as long as your data fits into a flat data structure.