me and my bro have only ever ran cut springs, i can't see any reason why its bad if its done right, yes cut stock springs will bottom out easyer and may fall out if cut to far for the shocker.
what we always do is cut stock spring with shorter shocks, to start with, then run a stock heavyer spring cut down out of another car with the cut coil of the spring flattend out to sit in the pearch like stock ones, then run shorter shocks to keep them captive, or make spring holders/tags at the bottom spring pearch like 4wd's use. the shhhocks always are better though.
also not all aftermaket lowered springs are heavyer than stock, so really you run into the same problems as cutting stock springs. ive seen it lots of times.
i would just cut them if your only droping a small bit, they should even still be captive.
hope this helps
cheers, dan