How to measure volume flow rate?

If it “Classified as Confined Space” you should a have it marked as such. You need to review OSHA requirements. You cannot “prove” natural ventilation when it is a “confined space”.
Positive ventilation and permitting requirements must be met. I worked in a company that had three “near misses” in confined spaces.

Dead people don’t go home at night!

I don’t know the regulations regarding air flow in confined spaces. But there are a wide variety of instruments you can use to measure air flow, ranging from fairly inexpensive to highly precise, very expensive. If you contact an HVAC company, you can probably have someone come out and measure it for you. Possibly answer some of your other questions as well.

It also depends on what is going on in the space and what type of equipment will be running. I once worked for a guy who was too cheap to hire or buy a gas forklift and ran a petrol one instead. His coolstore was closed by OSHA until he replaced it. I should have mentioned the lack of hygiene facilities when OSHA was there, but I liked my job despite the difficult working conditions. The owner was only pissed off because he thought an employee turned him in, so I thought it best to keep my mouth shut about the lack of bathrooms for almost 20 of us.

If you have an area that is “classified” as a confined space, then that is probably because someone has already evaluated its possibilities for ventilation and determined that there is insufficient “natural ventilation”.

To answer your question very simply: Yes, you need to provide positive outside air flow and exhaust of whatever fumes and gases build up in the room. (It doesn’t do any good to, say, position a fan in a doorway if it’s the only doorway. That doesn’t add much air inside the room; it just helps to move around what’s already there.

As long as it is a “confined space” then you also need to take other measures, such as:
– training the people who will work there in “confined spaces working requirements” and having a written policy for working in confined spaces;
– continuously monitoring air quality inside with approved oxygen level monitors;
– posting at least one person outside the space to monitor those inside, who can call for immediate help (probably from people with self-contained breathing apparatus) in case anyone inside is overcome. (It doesn’t do any good for a single person outside to attempt a rescue on his own and to be overcome himself; that just adds to a death toll.)

You don’t really need to measure “volume flow rate”, I don’t think. You need to assure that the oxygen level doesn’t drop below about 20%, that noxious / flammable gases don’t accumulate to dangerous levels, and that people know the dangers of working there and have “exit and rescue” plans.

You will need to meet code, which varies by jurisdiction.

From your description, I imagine solid walls on 4 sides, a solid floor, and no roof. Without any windows, you will get very little air exchange through just the roof. It would be extremely unlikely in this scenario that natural ventilation would be sufficient to meet code requirements, unless your walls are like 4 feet high. You should probably consult an HVAC engineer.