If passing visual isnt an issue, then you should be fine with headers and aftermarket cats provided your rear o2 sensors are moved downstream of the cats. Even with stock software you should get OBD2 "ready" state for your o2 monitors with quality cats installed.
Swapping to headers is very much worth the headache on these cars, made a nice difference on my prior 2.5L, I would think the 2.8 should benefit even more.
E46 330ci 6MT: BMW Performance SSK | 3.15 Diff | M3 Strut Bar | SS Brake Lines | Rogue Poly RTABs | UUC UDP
E92 335i 6MT: JB4 | DCI | CDV Delete | BMW Performance SSK
E36 M3 5MT: AFE Intake | M50 Manifold | ASC Delete | DDM Catback | Shark | Clears
E46 323ci 5MT: 330 Brakes | H&R Cup Kit | SSK | Clears | 3.46 | 18" CSLs | E36 M3 Clutch & LTW Flywheel