Rifters will get more scrutiny seeing as they are straight up strangers whose loyalties and abilities are a complete unknown. Ie they don't necessarily have any loyalty at all to the Chantry or the Inquisition and for all anyone knows they may agree with everything Corypheus is doing. Rifter mages are especially problematic because their magic doesn't work like Thedas magic, some of them (like Galadriel) are obviously very powerful in ways no one understands, and they're all apostates by default.

HOWEVER Cassandra will definitely be taking a look at some or all of the shardbearers too (she will be interrogating Sina, as soon as she gets back to Skyhold), so if there's a reason why your shardbearer might warrant a closer look or you would like them to be affected by this we can definitely make that happen too!