I can confirm this bug. Setting your private shop block to faction only, no enemies etc has no effect at all. Other players (non faction and enemy) can still use your shop.
Sometimes, once these settings are set, or you deposit money, then unload the sector by flying away or leave the game and then come back to the sector, the settings have not saved and the shop has reverted back to it\'s default state. This means you lost your deposited money, and lost the parts you put to the shop.
Even stranger is that the shop block that was placed is now gone, as the blocks placed on the planet have reverted back to a previous state (like that part of the planet was never edited), but the shop is still accessable. A ghost shop! It will allow you to place a replacement shop block on the planet, but then you cannot use the shop at all as it becomes errored.
Server (and client) is a clean install and a new universe with the release of 0.1401. (Really this is the second attempt at a clean install and new universe of 0.1401 on the server to try and solve the many bugs of the database not saving correctly and reverting builds and setting back to previous states).