Scry is the same level as teleport circle, so assuming people will never see your circle is poor security, no matter what mundane precautions you take against it.
Scry would only be able to help in an unusual circumstance. You can see creatures, but that only lets you learn the sigil sequence if the creature stays within 10' of the Circle for a full minute. You can see places, but only places you've seen in person before, so you'd probably already know the sequence. The only real time Scry would help is if you had been through the Circle before but were rushed through so you couldn't study it. Scry would let you go back and memorize the sigils.
if the defences are very effective, and the enemy can't simply infiltrate an agent, then an enemy who can and wants/needs to teleport into your temple will simply run the risk of teleporting in based on a description. The (probably not fatal) risk of a mishap when teleporting via description is much better odds than certain death via a trapped permanent circle. Especially, if the first person teleporting is a minion/scout; who can purloin an object, which the main enemy force can subsequently use to return via error free teleports.
Presuming that Private Sanctum hasn't been cast over the whole area, right? That defeats Teleport, Scrying, and most methods of observation from outside the Sanctum.
You raise a really good point though, that the defenses of the Circle have to consider the "substitution effects". Once you've defended the Circle enough to discourage its use by strangers (and encouraged them to use other means to sneak into the area) there's no point in defending it any further. Or being a hazard to yourself.
Good list, and excellent point that many destinations will have a mix of public and private spaces. The main weakness I see of having a relatively unguarded Circle in one of the public spaces is the change that a deliberate spy will come through already covered in Invisibility, Silence, etc. will be close enough to the sneak into the secure areas with the spells still effective. But I guess you run the same risk as someone just walking into the area and ducking behind a wagon to quaff a few potions, so maybe that's good enough.
Castle or Keep: This is the sort of place where you probably mix physical security with a social element - you put the circle either in an open area like a courtyard or bailey that is under watch of guards, or you put it in an isolated locked chamber with guards positioned outside and the best lock you can afford on the door, and you keep the sigil sequence a secret only a few people share. That way anyone wanting to use the circle has to not only know the right sequence, they also have to have a key to the door (because the guards specifically do not have one as a security measure), and be on the list of persons the guards aren't meant to sound the alarm at the sight of.
Good thoughts. Probably a room in one of the towers of the curtain wall, with very thick interior walls. That way anyone who exits the room would exit into the main inner courtyard where anyone on watch on either the curtain wall or Keep wall would be able to see them.
The party in one of my campaigns will very likely be making a teleportation circle on their airship permanent
Huh! I hadn't every thought of putting a permanent Circle in a thing that moves, but I guess there's no rule against it. Cool idea.