Syag,
If it sounded like I was suggesting that online sources are fine without exception or you can judge the website by how nice it looks then I apologize. What I am saying is that there are some excellent online sources, most of whom are regular businesses with an online presence. The sofrim or proprietors are known to be reliable or can be easily confirmed. You need to see if the website provides information about who they are, what their standards are and if they have recommendations from rabbanim and then you should do your due diligence and confirm that they are reliable. To repeat, choosing a source for STAM, whether online, out of town (ordering by phone) or a local source, requires research and consulting with rabbanim, particularly those who are experts in STAM.