We can't track the prior whereabouts of every single person across the galaxy at all times. Indoctrinated spies were a problem in the previous cycle. Letting people through simply because they don't have any documented time around Reaper technology is a sure-fire way of opening the door for such spies.
We don't need to track the prior whereabouts of every single personal across the galaxy at all times. This is what is known as 'letting perfect be the enemy of better.'
You're arguing against your own premise. If indoctrinated spies are a problem, then the logical conclusion isn't 'let through people simply because they don't have documented time around Reapers tech'- it's the opposite. DON'Tt let through people who DO have documented time around Reaper tech.
You can't stop the risks you don't know about- but you can manage the ones you do.
Anyway, Anyone who's passed through the Citadel or used one of the relays has been in proximity of Reaper technology, information that is published in the codex at the time of ME3. Everybody's a suspect.
Not all Reaper tech, and especially not the relays and Citadel, are indoctrination devices. There have been no in-universe indications of mass relays indoctrinating anyone.
It's a benefit because Shepard draws the "attention of those infinitely your greater" to any area within which s/he travels, and a lot of traveling is certain to be done (and is done) across all points of the galaxy.
Except Shepard doesn't go across all of the galaxy. Shepard doesn't even go to a majority of the galaxy. And Shepard, being in a stealth vessel, is one of the least-attracting things around- hence why Reapers don't automatically come after you in any system you enter.
Shepard isn't going to 'accidentally' stumble across a deliberatly secret project any more than Shepard accidentally stumbles across the Crucible project, or Santcuary, or Cerberus station, or the Leviathans.
You're going to have to show your work on that, because it appears as if Shepard travels through many of the active primary and secondary relays across a rather wide spread of the galaxy.
ME1 codex alone establishes that 99% of space is unexplored, and we also know the that the places that Shepard does go are a non-exhaustive list because new systems with long-established colonies pop up all the time both across games and within games themselves.
'Primary relays' are irrelevant. The hiding spaces and working shops wouldn't be in the systems of any relays- they'd be in dark space or useless star systems some way off the network- like Cerberus and Geth do.
Incorrect. Telling someone where something vital is and to avoid said area will reduce the risk of drawing attention there. Like painting a wall or a canvas and telling someone to steer clear. They probably won't touch it anyway, but it's better that they know so they don't accidentally bump into it.
A warning sign isn't a means to hide something- it's a means to draw attention to the existence of thing. The only use drawing attention has is as a distraction from where you don't want them to look.
Hiding from the Reapers requires not being seen- not putting out warnings to VIPs of 'there's something very important right here.' Unless Shepard is going to be in proximity of the Arc as a given- and there's no reason to believe that any more than Shepard discovering the Crucible or Atlast Station or any other black project by accident- spreading the information unnecessarily only increases the risk.
Shepard wouldn't be looking for the ark project. Shepard would be steering clear of the ark project.
Shepard would already be steering clear of the Ark project unless Shepard was deliberatly looking for it. Shepard arbitrarily going his way to steer clear of arbitrary space would itself be an indicator of something to notice.