I've debated this point in multiple forums. I think these are the issues:
Looting is an unbalanced element introduced into the ShadowNET living campaign. Characters can become 'unfairly wealthy' by looting things from the mission. This gear then becomes a monkeywrench for the next GM.
Changing ownership takes a long time (typically 8-12 hours). This is a downtime event and not action related, thus detracting from the real time game mission event. This creates extra bookkeeping for the GM after the event or a private session to resolve.
Aside from all the RFID tags and other tracking possibilities, the German version of the rules says that the device must be connected to the matrix for the entirety of the hardware test, i.e. 8 to 12 hours where the owner can immediately locate and report the device stolen.
The first pass solution to this is to simply declare in the job offering whether or not it is a looting or no looting mission. However, the specific solutions to the above issues are as follows:
Very often, missions end up being much harder than advertised by the Johnson. The Johnson offers a certain amount based on the rewards guidelines, but due to events in the mission, things get much harder and should be worth many times more. The added difficulty rewards can be in the form of loot, especially if the loot is what made the job more difficult in the first place.
Submersion and Initiation are already handled as private sessions. There's no reason that ownership conversion, or armor conversion, or equipment acquisition, or contact 'fluffing' can't fall into the same category. Looks like that's a once a month rule, so that in itself limits the looting significantly.
I'm still waiting on an official ruling from the developers about the intent of the always online rule. Personally, I see it as a way to put teeth in the glitch mechanic of notifying the authorities, since it was mentioned specifically in the same breath as the glitch rule. Nevertheless, there are still many tracking issues that need to be resolved in the specific mission before loot becomes 'safe' for processing. If those issues aren't addressed, any number of complications could arise.
Personally, I'm in favor of looting. It exists canonically as pretty much all the criminal element conduct hijackings. Within the setting, it therefore must be possible to actually loot. However, I also fully support any GM that doesn't want the hassle of looting. That's why I suggest the first pass solution of stipulating whether or not looting is allowed during a mission. i.e. Players may engage in looting at the discretion of the Game Master.