It's becoming rather annoying to keep all items on the guild floors, containers would be better, but I don't know which of them respawn and which are safe. I know there is a way to get information about selected items through console by typing "ori", but this only shows the item's ID and which mod it is from. In Oblivion there is some identifier program which allows you to see more details about the item (including whether the container is safe for storage) by clicking Alt + Right mouse. Is there anything similar for Morrowind?

For example, are containers in your manor built during the Houses' questline safe?

Well, as far as I know, almost all containers in Morrowind are safe. Basically the only ones that respawn are Guild Chests (eg. containers flagged as "organic" in the editor, obviously used for plants too).

Still, be cautious where you put your stuff. If you place it in a container that belongs to someone, it's contents will become marked as stolen.