I just got back from getting smog check. To answer the above question exhaust breaks aren't a problem as I have a PacBreak.
I PASSED the smog check and here is the information on sheet as it applied to my 2001: (I tried to duplicate how the sheet visually looked as best I could)
Overall test results - Pass
Comprehensive Visual Inspection - Pass
Functional Check - Pass
Emissions Test - N/A
Emission Control Systems Visual Inspection/Functional Check Results:
PVC - Pass Air Injection - NA
Cat Converter - NA Spark Controls -NA
EGR - NA Vacuum Lines to Switches/Sensors -Pass
Wiring to Sensors - Pass Ignition Timing - NA
Fuel Cap Visual Test - NA EGR Functional Test - NA
Fuel Cap functional Test NA Fuel Evaporative Controls - Pass
Fuel Evap Test - NA Oxygen Sensor - NA
Thermostatic Air Cleaner - NA Carb. /Fuel Injection - Pass
Other Emission Related Components - Pass
System Malfunctional Light - Pass
Liquid Fuel Leaks - Pass
ASM Emission Test Results - everything under this section was NA applies to gassers
Before I went down to have check the only things I took off were the VanAken (even though it has CARB D-500 number) and the boost fooler. Also note that wastegate is plugged. There was no question on the ATS air horn, AfE air cleaner, PacBreak, trans controller, gages, etc. The only thing that was even looked at twice was my breather, and that was because I trashed bottle and moved it over to driver side with a K&N baffled breather to eliminate climbing under truck, misting and draining which is now done by a tube in fender well. He followed hose over to breather watched that, saw no smoke and moved on. My suggestion is to go to a shop that has diesel knowledge. This shop raced diesels in Pikes Peak and off road. I think that way you won't have to go over thing like "whats that" on 2 low switches, exhaust break, 4" exhaust, etc. I think most will pass this worthless test and panic is for naught.
As you note in my input above the VanAken has a CARB number on it and is ok on 1998 1/2 to 1999 trucks, but since I have a 2001 I took it off. I questioned this with the shop, since the engine is the same is it good assuming it will pass snap test? Their response was this crap is so new they couldn't give me a definitive answer. I'm in the process of contacting VanAken for their take on this. If and when I get something back I'll post.
Good luck and I'm glad I'm done Oo. Just my $. 02 worth.