I've gone to a State facility every year w/ this setup:
BBK LT headers
BBK catted H
Flowmaster 40's
all emissions related parts/vacuum lines deleted from the passenger side of the vehicle, including rear crossover tube removed from heads
smog pump hooked up w/ custom air tube that plugs into BBK H
timing dead set back to 10*
running 91 octane
engine up to operating temps and not turned off at all while waiting in line
I've passed every year with no issues at all as far as visbility checks. They have used the mirror underneath and also popped the hood (sometimes) and nothing was ever questioned as far as the other pieces being deleted/gone. Do you really think every DMV Inspection employee knows what to look for on every single vehicle? You're lucky if they even know how to read any smog/emissions decals applied by the manufacturer under the hoods... As long as they see cats, a smog pump (if applicable) and the car is not some Beverly Hillbillies Hoopty, they usually won't question anything.
I only had an issue in 2008 for failing emissions a few times for high HC's, due to forgetting to bump timing back, running it w/ "regular" fuel instead of 91 or higher (Cobras have to be run on 91 or higher octane per the owner's manual), the ECT sensor was original (failing) and the car was not totally up to normal operating temps at all (it was only a 5 minute drive from work over to the inspection station). Other than that one minor issue, I have every single prior year's State inspection report showing it passed and nothing has ever been questioned as far as visibility checks.