After Psi Corp war, The extra reeducation camps were found out about but what happened to the Motherships and the colony on Arisia. Things that only the top people knew about.Considering that about the top 10%(?) of Psi corp where charged as war criminals and undoubtedly deep scanned.
Motherships: Well, sure the winners of the teep war know about them - as you mentioned. But they would not want this knowledge become public - after all, the government didn't, couldn't admit to their existence before the teep war (because they were basically illegal - the Psi Corps charter disallows Psi Corps to have armed ships of that size); and as anyone knows, governments prefer to sweep their past "questionable actions" beneath the rug. Sooo... officially they never existed; and those with a high enough security clearance to know about them (I'd say, ship captains and up) would have orders to make sure it stays that way (including "disappearing" any such ships that would happen to appear somewhere).
All that makes those ships outcasts of the most desperate sort... however they are also certain to have their own contacts within EA society (raiders that do business with them, Corps-friendly teeps that weren't caught, etc.)
Arisia: (from the galactic guide) "As of 2262, Arisia III is abandoned and suspended in a legal limbo, as Marcus Cole has never sold or passed on the mining rights to the world.
See? The shadow attack wrecked everything, and as of 2261 Marcus is unable to pass on the rights (being "mostly dead" and cryogenically frozen). I suppose some years after that the legal situation will be resolved - most likely the government (EA or IA) will nationalize the mining rights (placing a purchase price in an account accessible by Marcus when and if he's ever revived) and re-sell them to the next enterprising mining company. Most likely that will happen after the Drakh plague is defeated - before they really have other matters to occupy them - first the rebuilding after the civil war, then the Teep war, and then mentioned plague.
One question, can a teep on sleepers still block scans? If so are their defenses weaker than when they have their abilities?
Yes and yes.
Since non-teeps can block scans (the Garibaldi assassin in S-5), teeps on sleepers can so too (and probably better since they had better training and better understanding what can foil scans).
However, without tepelathy a teep would have to resort fighting a scan "in his mind", while with telepathy a teep could block a scan from even entering his mind, so their defenses would be very much weaker.
What sleepers would do nothing agaist would be mindblocks. If a P-12 block were to "lock" some memories (like Bester did to Garibaldi after Edgars) it would take an teep of equal or greater power AND skill to get through that block (like Lyta did with Garibaldi for NumberOne); no matter if the block was on a mundane, teep, or sleepered teep. And one could expect those people in Psi Corps to know the really good stuff to have the very best blocks available to keep these secrets even against hostile deep scans...