In our D40s in Australia we have two filters that fit into a slot behind the passenger side glovebox. We have to remove the glovebox to get to them. That's the only filter in the air path. If you drive without the filter (sometimes called a "pollen filter") the only issue is that you have no filter removing fine particles from the incoming air.
There are a number of possibilities though, given the experience I've had with our other car (which we bought second-hand for a low price and then found out why). This car had been parked under a tree (bottle brush tree, an Australian native with fine leaves that easily make their way into the air ducts).
This car wasn't blowing much air at all, and after opening the air duct entry in the cabin I discovered that the ductwork was full of leaves. Ok, clean them out - air now working - or so I thought.
The evaporator, when the airconditioning was running, would freeze water that got onto it (which is why these things have a drain to the outside of the vehicle). Unfortunately the evaporator also had a fair amount of dirt in it (we gathered that the car had been in water up over its roof, but this wasn't disclosed to us before purchase). This dirt combined with the water would freeze up and block ALL the air flow. Once the ice melted we'd have air again.
It's possible that the dust has gathered on your evaporator, and/or on your fan, and is what's causing your problem. In our little car, I placed a bucket under the opening and used a fine stream of water aimed up at the evaporator to wash out the dirt - this worked, and I didn't fear destroying things because the system is designed to have some water passing through it as humidity condenses on the evaporator and drips off, running to the drain and then outside.
I do not know if you could do the same. It's fortunate in our car that the evaporator sits vertically and immediately beside the opening, so I could squirt the water in and wash it. I'm not sure the Navara air path works the same. An inspection camera may help!
