There are many ways to estimate the air temperature rise in a sealed box, but it's not clear how you plan to make design decisions with this number. It doesn't mean very much by itself. I would think what you really need to know is the temperature of the electronics (die or case temperatures).
Most components specify "j-a" in natural convection, but that assumes a single component and no obstructions to natural convection, radiation, and pcb conduction. Don't assume this j-a applies to your situation!
As was said, without a fan, hot air will stagnate at the top and only a fraction of the enclosure will be effective for heat transfer. Perhaps you can estimate this temperature but this doesn't tell you the air temperature near your critical components and just as importantly, it doesn't tell you what the natural convection airflow is near your components.
A resistor mock-up that approximates your component layout will give you a pretty good idea of what's going on, tho it's difficult to mimic radiation and pcb conduction with resistors.
I know you want a rough estimate but without real parts the only other practical way I know of is to make a CFD model (full disclosure: i do this for a living). A CFD model can mimic the actual components, pcb layers, enclosure, fans, vents, etc. You can run various scenarios to see the effects of fans, heat sinks, etc, on the die temperatures.
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