It's almost impossible for someone to identify who has been accessing darknet sites. IF someone is monotoring your internet then all they could see is that you were using Tor, nothing else, they couldn't see what you were accessing just that you are using Tor so for that reason I would think that selling legal things on Silk Road would not make you a target, they have bigger fish they can't find to try to find first. lol Considering that SR isn't even one hundredth of the global drugs market I really don't believe much time/money are being spent on bringing it down.
I might be wrong but just thinking realistically, without my paranoid hat on. I've ordered small quantities of cannabis from there and some ebooks not once something didn't arrive and I got a refund.
Yet to try Atlantis though want to try it out with litecoins. Both sites have a ban (rightly so) on selling guns and child porn, other than that it's the only free market place which is an important thing to keep alive.