You generally don't carry the house deed with you. If you want to buy it and not place it right away, you can put it in your bank which is safe from other players. Then you get on in the dead of night, go to a tiny town nobody uses, get your deed out of the bank, recall to the site you picked out already, and plant the house. It should take seconds.
If you run around with a house deed in your pocket it's like having 50k to 1m gold just waiting to get stolen.
The runebook thing isn't an issue. You should be able to make copies of all your runes, so you will have a couple spares in case anything goes wrong. The main issue is that you generally have runes to cool places you don't want anyone else going, like a neat spawn you found or in front of your house. But depending on how easy it is to get into people's houses - such as with lockpicking - and how much they can do once they're in there - meaning, can they steal a locked-down furniture, do you store valuable materials in your house, how good are you at hiding those materials - losing a runebook might be little more than an inconvenience.
For example, let's say you can lock down a table and nobody can pick it up or break it. That's a pretty good security system: put a pouch on the floor, your metal or wood or whatever in the pouch, and lock down the pouch, stick the table on top, lock down the table. Even if they know the pouch is under there they can't access it.
You can also just keep a lot of crap in nested layers of chests, boxes, backpacks, bags, pouches. You know exactly where your good stuff is but it's possible nobody would bother looking through all that.
Part of the fun of the game is figuring out little tricks like these. They emerge not because someone coded them in, but because you can observe behavior in the game and you have enough control over stuff to be able to take advantage of it. It also means playing with friends is a LOT of fun, and having a mentor is pretty helpful.