I wouldn't call the contents of this box a "whole mess". It looks complex but there's nothing really weird in it. Power enters the box via cable 7 and energizes four circuits:
- Unswitched power is permanently provided to circuits elsewhere
in the house via cable 5. This circuit is slightly strange as both
the red and black wires in the 14/3w cable 5 are hot, where ordinarily only one would be used and the other abandoned.
- Switches 3 and 4 (as numbered left to right) control the motor
and light of a fan on the other end of cable 6.
- Three-way switch 1 and a three-way switch on the other end of cable 2
control the load on the other end of cable 3. (You believe this
circuit may be disabled.)
- Three-way switch 2 and a three-way switch on the other end of cable 1
control the load on the other end of cable 4. (You believe this
circuit may be disabled.)
Switches 1 and 2 are both still fully wired. When you toggle a fully wired three-way switch and nothing seems to happen, you have encountered one of several situations:
- A load is being switched but you haven't found it. Often this is an outlet with nothing plugged in, or a lamp that's locally switched off.
- A load has been removed.
- The other three-way switch has been removed and its wires capped off. This will leave the load permanently without power.
- The other three-way switch has been shorted or replaced by a wire nut, that is, both travelers have been permanently connected to the common. This will leave the load permanently powered on.
You can do some further analysis. Disconnect switch 1, and check which travelers in cable 2 are hot.
- Neither hot = the other three-way switch has been removed and its wires capped off.
- Both hot = the other three-way switch has been shorted or replaced by a wire nut.
- Only one hot = the other three-way switch is still installed.
Do the same for switch 2 and cable 1.
However this doesn't help you very much because if you want to be code compliant you still have to locate the boxes at the other ends of cables 1, 2, 3, and 4 so you can make sure that they are safely and properly decommissioned. Abandoned wires must be separated and individually capped. As jbeldock says in his answer, an abandoned switch must be removed and the space covered with a blank plate.