[Captain Kwok]

A ship will take any supplies/ordnance that it needs from a planet regardless if a Resupply Depot is present, assuming it's in the sector during end turn processing.

As I mentioned earlier, the extra supply/ordnance is for resupplying the odd ship that needs it before a resupply depot is constructed. If you give the AI a low bonus, the few extra components make no difference in construction times.

AI colony ships do on occasion pick up Weapon Platforms, depending on their destination and if a WP is easily available.

Damaging warp points can do 100-200 damage to a ship. Without a few armor components, a colony ship could lose most of its components (particularly engines) quite easily, leaving it to limp along to its target.

Colony ships are not ordered to dangerous systems, but occasionally they end up in one because it's on the way to a non-hostile system. There's no way right now for the scripts to know what systems a ship has to go through to get to its destination, so you can't always stop a non-combat ship from entering a hostile system. I've requested a script function to provide a list of systems that a ship has to travel through, which will allow a check against hostile systems etc.