No ships can be modified. However "modified" or "Variant" versions of ships may become producible. In the future with the release of Research and Development read rules here
you should be able to make a slightly different version of the ships for which you have Data cards. If you dont own any data cards you will probably have to research and unlock them.
They are calling these "Variants"
You will not be able to increase your personal Bff-Bulk speed from hyper 4 to 15, but just guessing perhaps with engine research you might be able to produce a ship datacard that is a speed or two above standard and will be able to produce BFF-Bulks with hyper 5, or perhaps sublight of 40 instead of 20. Or maybe you put research into weapons and you are able to make a Variant BFF-Bulk datacard with two turbolasers, for whatever reason. I still consider this modifying ships, but not in the way that a lot of new players care about. It will likely take a good deal of time and resources to gather enough research points to make Variants anyway.
Nothing major, to keep the game balanced.
edit: I suck at hyperlinks