Im still working on my prep for "into the maw", my first attempt at GMing and also Rogue Trader.

However ive hit a small problem. In the scenario when the players are "ambushed" in Port Wander the enemys stats are very close to the players. And going by the characters they are going, if i take into account armour and toughness damage reductions they they are going to have a hell of a time taking them out. This will also be the same but worse with the Orks at the star mirror later on and their toughness bonus of 8. The only player i think who wont have a problem is the Arch Militant with a hellgun with its Pen7.

So how do you all run this? Do you just allow armour damage reduction and run it that the NPCs are simply weaker and less tough than PCs?

From my experience of D&D, enemy NPCs were always much weaker than PCs (but more of them) with the exeption of bosses or sub bosses.

Try not to worry about it. Rogue Trader enemies are powerful, and the combat system isn't geared towards mass-scale combat. PCs having Fate Points is another large advantage, and if they get taken out then they'll burn a Fate Point and you can have them survive the scene. Alternately, once the escape attempt is made their attackers could disengage since their "job is done". If you get the Koronus Bestiary the things in there are terrifying, so if your group has trouble with a random ambush in Footfall this could be a good wake-up call for them.

As your players level up they are going to dramatically outpace huamn NPCs, and then various Xenos NPCs, and then your Arch-Militant will regularly challenge and destroy Orks at arm-wrestling competitions and you'll wonder when your game spiraled out of your control.

The closest I've ever come to a TPK was during a fight that I thought would just be a quick, simple affair that the dice disagreed with. You're free to alter encounters however you see fit (for YOU have the power), but don't be afraid about challenging your players. They might surprise you.

Im not so much worried about them surviving, they are experienced role players and I know i can "fudge" the rolls to make sure they survive. Im more concerned about the battles being too drawn out and boring to the point of annoyance. For example if a PC rolls an 11 damage (9+2) they have nearly maxed out their weapons damage, but only do 3 points of damage once you take into account the oathsworns toughness and armour. With the oathsworns wounds of 18, they are going to take a while to take down especially with 1 per PC. Compare that to pathfinder where weaker enemies can be killed within 2 or 3 normal hits, especially if you crit.

I think for now ill ignore NPC toughness and just use armour since it varies with location. Once they start getting too good, ill use toughness also. My logic being that at the start they are dealing with gutter scum for hire who are not on par with our "chosen people" PCs, but as the difficulty increases they encounter a better quality enemy who are more akin to themselves.

Typically you would use mook rules for most NPCs, while your elite/boss enemies get their full stats; the basic version of it is that any shot that gets past the armour and toughness of a mook is enough to kill them.

Well Oathsworn Body guards are exactly that. They are sworn, highly trained, superbly equipped loyal body guards. While gutter scum are exactly the opposite. They have stats for scum type NPC's, called "Hired Guns" and "Scums." (pg 370 RT) Their armour is 0 - 2, T bonus 3, and wounds 9 - 12. Compare that to the Oasthsworns armour of 6, T bonus 4 and wounds 18. Just saying.

And fyi, don't worry to much about the PC's not packing enough heat. They can acquire Starships, so acquiring pistols with manstopper bullets should be no problem.

And fyi, don't worry to much about the PC's not packing enough heat. They can acquire Starships, so acquiring pistols with manstopper bullets should be no problem.

This has not necessarily been the case in my experience

For example if a PC rolls an 11 damage (9+2) they have nearly maxed out their weapons damage(...)

Uh, did your team forgot to write down the weapons they get at character creation? Why are they using laspistols?