TL;DR: To slow the intruder down.
Step back in time for a moment and imagine you're one of the Dwemer. You need a way of being able to access a room that makes it hard for other people to get in.
You could put up a gate with a lock, but this has several major flaws:
- People in Skyrim know how to lockpick.
- People who need to enter the room need a key.
- People who want a key can pickpocket someone who has one.
- People who want a key can kill someone who has one.
Now consider putting up a system that requires people to move levers around in the right order:
- Cannot be lockpicked.
- No need to forge a new key every time.
- The correct order cannot be pickpocketed (unless written down).
- People who want a key would have an incentive to keep you alive.
Someone could figure out how the system works, but remember at this point in time the mines are still fully operational. That means there are Dwemer walking through the corridors all the time, so the longer an intruder takes to figure it out, the higher their chances of being spotted are.
These are the same reasons for why people use combination safes instead of safes with keys.
Now look on the other side of the coin, imagine that humanity died out and the apes took over. You are now an ape trying to break into fort knox. Fort knox stopped being manned centuries ago but the ruins still stand. It would take you a while and you might need some heavy machinery, but you'd eventually break in.
When it comes down to it, all security systems are just delay mechanisms.
Even passwords. Given enough time, a program set up to brute-force your password will find the correct password evantually. The idea is to make it take an implausibly long time to brute-force, not to make it impossible.