It seems that some weapon mods aren't showing in the weapon mod menu for me.

Weapon mods like the Laser RCW Scope and Plasma Defender External Heatsink aren't shown when I try to mod the appropriate weapons.

WMX is up to date and I have the correct compatibility patches for PN and other mods.

Could it be that the maximum of 3 weapon mods on any weapon prevents more than three showing in the mod menu?

It does, as that's how maximums work. That's not what's causing your issue, though. Please see the WMX FAQ.

Some mods do have duplicate weapons too, so though they may be named the same they can be different, and thus take different mods. Like WMX-MW and PN both have a Desert Eagle and Classic Fallout Weapons and PN both have Wattz laser weapons.