agreed. showing only the weapons of the currently selected group might be a good idea even for the current weapon group mechanics anyway, since it's usually unnecessary information during combat, and could be removed/reduced to clean up the UI a bit.
non-selected groups could still be displayed with their respective numbers, status of autofire and alternating fire, and maybe something simple like the total number of weapons in that group (or total of each type, so that a group that has only missiles in it would clearly show as such). that would be more than enough info for a player who created the loadout, and would still clearly show how many other weapon groups there are to select for someone who is not entirely familar with the loadout or even the concept of weapon groups itself.
and since weapon groups can be switched while the game is paused, even if the player has no idea about what the different groups include, it's easy to just switch between them to get info on all available weapons. in fact, it might even be easier to figure out the content/purpose of each group if the information is a bit more 'focused', rather than always showing everything.
even with all that said though, i don't think showing a weapon in more than one group in the current UI would really create problems in practice. most weapons would still be in only a single group, and crazy edge-cases like your Onslaught example are already possible by dividing the weapons of one type into several groups.
for example, on an Onslaught with Mjolnirs, Heavy Needlers and Light Needlers mounted on the 'nose' and 'arms', you could use 3 weapon groups that each contain 1x Mjolnir, 1x Heavy Needler and 2x Light Needlers, to be able to control leftward, forward and rightward facing turrets independently of the other two directions. so even though these groups only include a total of 3 different types of weapons, the UI would still display a total of 9 weapons in individual lines.