One of the biggest issues with aging boards that have heat sinks and/or fans is the breakdown of original thermal compounds and thermal adhesives. Especially when on location for yrs from dust and grime.
The issues I correct with users adding fans is improper placement or the case designs that do not give any advantage by adding fans aka zero positive airflow. Most having exhaust fans, but extremely limited intake volume. (These are mostly hobbyists with little to no knowledge in electronics)
Another example is Naomi, its air circulation design is actually more than adequate, the true flaw is the design of NU/NC/NNC most of these systems were in, with OPs in most cases, not having a regular cleaning schedule inside these cabs. The intakes easily get clogged and the components weaken over time from heat stress.
Another sad reality is a large amount of systems like Chihiro, Naomi, and even Lindbergh. The components are severely weakened from heat stress by the time they reach hobbyists.
Most locations around the world, regular staff only wipes down machines. Techs only clean inside when a machine breaks down. On our locations, every 6 months after hrs, machines were pulled and cleaned. Especially ticket redemption, due to the addition of ticket dust.
It sounds like your cleaning routines are pretty solid. A lot of the cleaning really revolves on the environment as well. For example, here in Japan you could smoke at almost any arcade and they were packed with people. The tar in the smoke mixes with the dusty air and humidity causing a sticky cake like substance to clog the machines all the way around. Ive come across so many machines Ive repaired where Ive taken a plastic scraper to remove the sticky goo from fan blades and casings.
The reality is that most of these games were never intended to last for as long as they have. Some manufacturers cut corners intentionally by not adding extra parts (i.e. fans or bracing to stop pcb flexing, using cheap parts which eventually failed meaning the manufacturers had to repair them at a cost, using bad solder which cracks leaving chips that literally fall off the board (sega hikaru bga) or even ending services (like sega and there satellite service) and even going one step further with having to return a key chip for example Ringedge hardware.
Going back to fans.
Having a fan directly pointed either over top of a heatsink cpu or from the side serves a good purpose of creating a stream of air cooling down the cpu. There is nothing wrong with this at all. Basically every PC set up has unless it is liquid cooled.
Sure if you just point a fan on random components that dont need it there is no point but having one on or near the main cpu is definitely a good preventative measure especially on components that get really hot.
As for Naomi systems they specifically will not turn on without the cpu fan connected (on a good naomi). Its a preventative measure because without it the cpu lifts off the board. I have personally repaired over 100 naomi 1 boards and still own 22 of them.
What happens when these machines are left on site without regular check ups is partially what you said. The people running the arcade dont know how maintain them which causes problems like exhaust fans get clogged and hardware hanging in a stuck state until someone catches it or even fires or blowing fuses.
On pc hardware this is more aparent and detrimental to the survival of the machine. The big killer is when the cpu fan gets stuck and the machine
isnt turned off right away. It sits there baking itself until it burns up.
When you look at the datasheet of ttl, cpu, buffer, etc. It will tell you the optimal operating voltage and temperature of each component so the user knows what it can handle and what it cant.
Some manufacturers know that running a particular chip i.e. a voltage regulator with a small heatsink isnt optimal but will do the job for a while and choose to do it anyway because its the cheaper route or adding a larger component wont work wit the original design etc. The result is that it may push the optimal temp range more toward the hotter running side and limit the intended life of the component.
Going back to the cabs on site.
The other thing is that once the machines are turned on, there are only a few people to walk around the entire place sometimes. If a machine develops a fault and is turned off quickly there is a much better chance of saving it. If the machine is left on with the fault, the chips begin to break down, burn out and lift off the board. This combined the the above can kill a board.
Im not sure how familiar you are with the chihiro but the biggest problem when the cpu fan dies on that is the cpu overheats, warps, and rips the traces from the board. Once this happens they are unrepairable. Constant and reliable airflow will keep these running well for a long time (or until the caps need to be replaced)
Vegas 777 hardware like Carnevil has a fan mounted 7 inches away from the board but pointed directly at the cpu to cool it down.
So the bottom line is that if you have any arcade hardware that uses a fan it should be maintained regularly. Boards that dont have a fan but should have one and are run without it may experience trouble down the road. As for my stance on the JP3 boards, like I said before. The one I have where the heatsink came off the cpu was getting very hot. Adding a little air to it doesnt hurt but this is just a suggestion for those who feel it will help.
People who can repair arcade hardware (especially older stuff) are becomming more and more rare. You have to learn how to keep your hardware running for as long as you can with whatever means you have unless you want to pay the big bucks down the road to have them repaired by someone else.