You know I was thinking about this the other day. Piracy is a good reason to have it on-board.
In this future there may be a government mandate that all civilian ships must have a self-destruct system in place for vessels that have the potential to carry hazardous materials. If a freighter looses propulsion and/or navigation control and endangers populated systems, this would allow the destruction before coming into contact with said area.
Another reason would be to safeguard populated areas from nuclear radiation and destruction. According to the Self-Destruct Warning sign (see below) it has "Nuclear Bolts". This means the Nostromo has a nuclear reactor. If there was a reactor leak and threatened civilians, the ship could be moved out of the habitable area and detonated if the situation is unresolved.
Also because it has a potentially dangerous nuclear reactor, the owner/government would want a system in place to prevent theft of this power source going into the wrong hands.
Really it would be good to have this on the ship for all the reasons you can't think of in advance.