SQL and DBI are meant to provide an easy to use interface that saves you coding time. Most database applications require far more time to write by hand than is taken up by all the queries conducted over a year plus. The big question is, do you need that extra speed here? Is maintaining and updating 3000 files worth the extra coding time? In this case, probably yes, since you're already doing the primary database work and just want efficient searching of data. You could, however, put all the data in one file, with a secondary file showing start and end locations for each question set. This would leave you most of your speed without requiring thousands of individual files.
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