Hey folks,
According to TOS the nevigation delflector actually projected out ahead of the ship and cleared a path. It is likely that the slug throuwer would work if luached from another vector.After all, ships seem to ram each other without the navigatorion deflectors getting in the way. I'd have the weapon do damage as per a ramming object. Probably Max damage would be for a Size 1 object at .98c.
I ran a species (the TORDON) who used a similar weapon (rail gun) that way. They were rather nasty until the PCs though up some decent counter measures. A few are: tractor beams, travelling at high speed, and counterfire.