Im wondering if this fee in Dubai is something fairly new?
Its been a few years, but I used to transit Dubai with all sorts of "controlled" items (body armor, helmet, weapons parts, magazines, etc..)... Typically when going through Dubai to Iraq I only had a 4-5 hour layover... When going through Dubai to Afghanistan it was typically 24-48 hours though (we used to process our entry visas into Afghanistan at the A'stan embassy in Dubai and it would take at least a day, sometimes 2...)..
I never paid any sort of fee.. the police would meet me at customs, have me bring out my "stuff" for them to inspect.. then they would take it and store it in the police holding area for however long I was going to be there (to include even a 4 hour layover).. A couple of hours before I was ready to board my flight, I would just hand the gate agent my receipt from the police, and they would arrange to have my "stuff" moved from the storage locker to the aircraft...
Never once did I have anything go missing.. and never once did I pay a fee..
Granted, I wasnt transiting with an actual firearm or ammo... but there were literally hundreds of people doing this exact same thing every day back then with other items the Emirates wouldnt allow in their country .. and the police had the transaction down to a science.. it was efficient, easy, etc.. and they were always cordial, and reasonably friendly, etc.. I dont think it ever took me more than 20 minutes to hand off my stuff, or more than 20 minutes to get it back onto an aircraft..
I still transit Dubai at least once a year (sometimes more).. but havent taken any controlled "stuff" through there with me in probably 6-7 years..