I have drilled the pipes on many Intruder 800s, including the two I owned, and never regretted it. The first one went 135,000 miles, and the second is pushing 60,000 already, so apparently there are no ill effects. However, wait until after the first service before you do anything to the bike.
If you are worried about drilling, check EBAy for a set of used stock Intruder 800 mufflers, which can be had very cheap. They are identical to the ones on your S50, so you could drill the used ones as a test. If you like the sound and performance drill the originals and swap back, and if you hate it put the unmodified originals back on. Either way, relist the used ones on EBAY and the test shouldn't cost you anything other than postage.