All effects are client side, so in theory (and with permission) you can simply edit the inis to suit your needs. I remember once I made all the codies (through about 3 hours of editing) have a single green-ish ball effect that I believe the JADE has.
That said, The issue can be corrected to each players needs by themselves aslong as they have permission from the devs and admins to do so. I'd turn it into a business with ships skins and all, but for 2 reasons, I wont;
1: Too lazy.
2: Lost all my tools. 1/2 of which, cant be replaced because they were from the old Lancers Reactor.
A General rule of thumb, however, is you only mod how the thing looks. No changing models, no changing stats. Also, the appearance cannot affect gameplay for either better or worst (IE, a gun that fires "invisible" bullets or a gun that shoots uber large projectiles).
