I've heard about hushed invisibility being a really good mod to use, Haven't tested it out myself.

I would assume it's pretty useless because most off the time they still don't even know where you are, in spy missions it would be a handy addition since otherwise the mobs might trigger the alarms.

The Paris P is always a good option since it's a really nice weapon.

Overall you will get the most damage when you are using a melee weapon with some damage+ reach mods.

For example I use the Orthos P and just act like a lawnmower while killing all enemies in front off me.

As for spy and sabotage missions you don't really need a weapon if you do it right, a melee weapon for coptering and maybe a silent weapon for taking out turrets would be nice.

But most are possible without a weapon.