I would suspect that any programming software that was any good would be smart enough to not waste its time explicitly writing those bytes. If you want to find out, you should have no trouble simply deleting the lines in the HEX file that contain only 0x3FFF's. (not counting the colon, first 8 characters, or last 2 characters of each line, which are part of the HEX file format)
if you do that, you can then simply compare the time it takes to program the PIC with and without those lines included and deduce whether your software is bothering to write them or not.