Depends on the hardware inside.
A)The bottom fan is essentially useless:
-most chassis' 'floors' are just too close to 'the floor'
-fan filter
-fan grille(the size and shape of the holes)
-the psu shroud
The potential for air through there is pretty weak, unless you brute force it with high static pressure, high rpm fans = loud.
Remove it and make cable management slightly easier with one less cable.
B)3x top exhausts? Great for gpu thermals - screws over cpu air coolers if you're using one; sucking cool air away and out the chassis before it even gets to them.
Perhaps remove 2 fans: you won't maximize gpu exhaust anymore, but you'll improve airflow into the cpu air cooler. Pick your poison, I guess.
C)Did you test cpu, gpu, etc., thermals before and after the side panel mod to see how effective it is?
I did something similar with my H500P Mesh's top panel: removed the acrylic piece and fit a honeycomb mesh up there.
Some older pics - before I mounted the Kraken G12 + Celsius S36 on the 1080Ti:
Once I installed the Kraken G12 kit, the airflow in the chassis changed, and thermals were actually a little worse with the mesh mod, so I put the acrylic piece back in - I also took out a few fans, because they were just getting in the way.