is there a way to add sound suppression on an ARES Crusader II on 5ED?
The Ares Crusader II comes with a Gas Vent II system which is a barrel mounted accessory. The book states that this is an
integral accessory (Core 427), the integral part says to me it's part of the gun itself and thus cannot be removed (at least with the rules as provide in the books). As long as it has the Gas Vent system, it cannot
also have a suppressor, as each location can only mount one accessory (Core 431).
In Missions, I would say, "No, you can't swap them out." In a home game, I would probably allow an Armorer test to remove the integral gas vent system, and change the barrel to a standard barrel that can swap between various accessories... but the integral gas vent system would be garbage and if I wanted to swap a gas vent system back in, I'd have to buy a mountable one.
... what are the limits in modifying the module so it will still be legal.
There is no really good answer to this. Honestly, when I first started GMing for Missions, I went strictly by the book and didn't add a thing. A year later with two games a week and 4 day Convention under my belt, I am confident in my ability to tweak encounters to challenge the players while remaining well clear of just being a dick.
I would say keep any modifications light to begin with until you feel comfortable being able to gauge your party strength and what they can handle without needing the book to tell you, because man, Shadowrun is not at all like D&D with a sort of method to calculate Encounter Points or whatever, based on the combined level of your party.
As for the limits of modifying it? If you want to throw a dragon at them because that's what you want to do, there is nothing but your own common sense keeping you from doing it, really... as long as at the end of the Mission, their rewards are based on what you find in Picking Up the Pieces. No, "Well, you killed a dragon so here's another point of Karma not expressly granted by the Missions author."
I refer you back to Bull's rules, particularly "In Gamemaster We Trust".
Just keep within the flavor of the Mission,
tweak it if you wish, but probably avoid adding something that's completely unrelated to the run, and make sure their rewards are within the bounds of the rewards chapter. I generally allow looting up to about 10% of what they otherwise earned on the run. If something would push them 15-20% or higher in terms of fenced loot, I figure out a way to deny it to them... so that Cyberdeck got busted in half, the car crashed, etc.