Hiding your homebase location in the shop network would be moot, because it is still totally visible in the Faction info under the Diplomacy tab in the Faction window. If you were able hide it in the shop network, then you would need to be able to hide it in the Faction info as well, or those trolls will come to your base, even if you were hdden in the shop network.
As for other locations, the shops are as vulnerable to attack as any non-HB stations, and you would probably be as miffed about losing them as any other stations, if a troll came along and ransacked them. One solution would be to alter configs so that the shops are protected from harm, just like your homebase is, this would make them a less enticing target to trolls and thieves. I don't know if this can be done purely in config, as it may need recoding the game to make it possible.