I believe you can limit it by date as well, only load the last X months of data.
That is different data, separate from the star systems database that @robbyp was referring to regarding limiting the sectors with systems stored.
I already limit the date range of the history to be read and also limited the data types to just "all entries for statistics" - and still get quite a delay in starting up EDD - no problem, I just load EDD and let it do its thing while I sort out stuff. (There is a lag when changing commanders but that is not too long.)