Most people can not use teleportation like we do. There's a finite resource called Anima that is used up whenever someone teleports that comes back slowly. For most people, this finite resource means they can't just teleport around the realm on a whim as they might not be able to teleport back for a while. The WoL (and probably most people with the Echo and most people who are adventurers) has infinite Anima (or it regenerates so fast it might as well be infinite) so we can pretty much teleport as often as we want.

And yeah, individuals have to attune to an Aetheryte before they can teleport to it. So the concern isn't guarding the Aetheryte from people coming through the Aetheryte, but from people taking over the city the normal way.

The few times it seems we are teleporting to Aetherytes before attuning them is really a result of having access to Y'shtola. And it's not really an Aetheryte we're attuning to. It's one of the crystals on an Aethernet and we already have access to one of the other crystals on the same Aethernet. Y'shtola is boosting the aetheric signal for us which is mentioned to be very difficult to do the first time she does it (Titian Hard I think?). That part just get's cut out most of the other times it happens.

The other reason why teleporting in on an Aetheryte probably isn't done all that often for sieges is because it's tactically a very obvious thing to do. It would be a lot more surprising to take over something else before making use of teleportation. There's just so much that could go wrong logistically by sending people to an Aetheryte where it isn't known what's on the other side that I can see people writing it off almost immediately.