o/ Hello fellow Kaleun!
I run steam and SH3 and all the mods below no problem. So, yes I think what you are asking can be done because I am doing it!
As far as I know the steam version comes at the latest patched version of SH3 and I installed GWX3 Gold and then Subcommander accordingly right after that installation.
GWX - 16km Atmosphere
GWX - Axis Mediterranean Aircraft Skins
GWX - Enhanced Damage Effects
GWX - Late War Sensors Snorkel Antennas
LifeBoats&Debris_v4
Pascal_Port_People
Torpedo damage Final ver2.0
North Atlantic Green 1.1
GWX - VIIC41 Player Sub
Ice Age
Real Depth Charge
New_clearsky_clouds
New Uboat Guns 1.2
GWX - Alternate Loadscreen - Full Circle
GWX - Captain America's Officer Icons
GWX - Main movie - 'Das Boot'