I shorthop all of them. Fullhopping them leaves you more open, since you're not really cancelling the lag of the first missle. I use zair to approach, homings only if they're too far away, and I never use it on Lylat Cruise, since the tilting just causes them to hit the platforms. I do try to use more smash missles though, I really want to see if they have more potential than the crap that other people are giving it. It's a lot harder to cancel than homings, but the effect is somewhat greater. It's useful for offstage harassment, since homings often lose their trail and/or blow up too soon.
Does anyone remember the "Hylian lowrider" from melee? The ledgehop-super missle-ledge grab had a 2 frame window of opportunity and was extremely difficult to execute. It's a lot easier in brawl and can be used quite effectively. Take note that it's impossible to ledgehop super missle onto the stage, unless you're on Lylat Cruise and the stage suddenly tilts in your favor. Don't count on that though.
Retreating missles tend to slow you down more than you opponent. Retreating with zair is much safer than using homing missles imo. Zair lands 4%, homing missles land 5%. Not much of a difference and zair is easier to execute.
Samus is a beast in the air, not so hot on the ground, I take to the skies whenever possible to bring out my onslaught.