Themken: So should I go look for a different target if the ship has too many nasties the likes of sentry lasers and such instead of trying to fry off enough to get acceptable odds?
As you already said, the boarding model has been tinkered with between X3:TC and X3:AP. Since I've never done any boardings in X3:TC, I can't really say how bad the sentry lasers, hull polarization and other boarding defenses affect the performance of your marines.
In X3:AP, whenever I see a target with such an extra level of nastiness it's usually enough if I use more experienced troops and exploit the full number of marines that can be involved in a boarding operation - even then I might lose a couple of them.
So, it's up to you really. Extra defenses make things harder for you, but it's still not an impossible thing to pull off.
By the way, totally off topic, remember when we joked around about how a peace-loving Boron marine might sound during a boarding operation? It so happens that I found one left over in a ship I was boarding.
I've since used him in the lines of duty and I call tell you that I laughed myself to death the first time I heard that scared-anxious tone in which he cues the boarding milestones. Imagine an "I need more covering fire" uttered by a squiddie shaking with fear, or a "Deck 1 cleared! (but let me now hide under a command panel and never be heard from again)" and you'll get pretty close to the actual thing :D.