As of version 3.04 (March 2005), it should cause no problems- there have been few, if any, reported problems with having Hyperthreading enabled while using GS3.04. If in doubt, you can certainly try disabling Hyperthreading.

Although Gigastudio 3.04 does not directly take advantage of Hyperthreading, if you use VST plugins within Gigastudio, they sometimes take advantage of the other 'side' of the processor and thus a small performance gain is seen.