In my group we have a lot of situations where using ship bound weapons vs ground troops is strictly a good play, so they do. It's hard to CONSTANTLY come up with repercussions to prevent using this (On less popualted worlds, for example) strategy. Also, realistically a successful shot from a ship weapon doesn't mean a direct hit; it just means the shot was close enough to deal damage (Through explosion damage) but then taking full damage from the hit doesn't make sense.
Anyone else experiencing a problem with ship bound weapons being too good and having a solid way to deal with this?