I think it's not inconceivable that the all the Seekers might have lived too far away to make it to the shelters in time to escape either the Lindblum attacks or the flood of lightning. Or that with the exceptions of a very few exiles, the Seekers were all part of Lindblum, or some other nation hostile to Alexandria and thus would naturally also not get into Alexandria's shield to survive the flood.

Then again, we haven't seen a single Mamool Ja either in Alexandria or Solution 9 either, and yet from Gulool Ja's existence, we can make a reasonable argument that at least one female Mamool Ja must have existed there, until relatively close to the WoL busting down the door. As others said, we have only explored a really small part of Solution 9 so far... and at a time, when it would only be natural for the citizens to not feel like going out too much, so plenty of chance we might meet some Alexandrian Seekers later in the post-MSQ.