We just tried this, using the 1.5.8 business edition, and it did not affect order confirmation email transmission. Since we're newbies at HikaShop (but not at programming or web design), it's entirely possible we've not set it up right ... here's some information about what we've got:
On the System->Emails screen, there are a list of names; the third one is "order creation notification". The far right of the page has a column for "Published". Instead of a green check mark on the order creation notification row, we've got a red circle, which we interpreted as suppressing the email transmission. Doesn't happen, though.
I'll go in with PHPMyAdmin and see if I can zap the flag in the database, 'cause that does seem to work for other people.
BTW, you show great forebearance with those who are too cheap to pony up for your commercial versions - I don't think I'd be so tolerant.