They infested humans because they don't have the ability to infest ships or build ships of their own. The infected humans build the Nomad combat army. The Nomads themselves are squishy, although they emit something similar to shield it only takes one ship shot to kill it (in RP). The infecting of humans with opposabble thumbs and stuff gives Nomads access to metal ship with shields and tech and stuff.
If you play through the campaign there is no "infected" ships the way you describe them. Only infected human hosts who fly normal ships, the Scorpion is a Drone created by the Nomnoms anyways, not an infected ship.
The biggest argument for this would be the LNS-Tundra. As for a modeling issue, could be 'solved' by modeling weapons for Das Wilde that were 'infected'. Because of how they would attach it would look by extension the fighter was infected. However this has the potential of clipping issues.
I kinds see what he means have a ship like the wraith but have it Definitely Different from a normal wraith in some way nomad like engines maybe or a different Texture like the wraiths maybe?
i have some crappy as hell sketches i made of a Wilde Fighter and bomber line if only i could find them