Confusing question but in all theory...

1) If you wanna do this BEFORE a game even starts, the only reasonable way is to, indeed, make a custom map without resources. (You meant the bonuses like 'geometric' symbols of eco/mil, etc... right?) Unless, read on.

2) Hex editing a saved file! Although i highly doubt that would be a code compatible attempt as it most probably should screw up many other things in the gameplay processing such as Ai ship routes_paths and grid coordinates flow which are ALREADY active by logarithmic calls. Messing with that stuff may give out lots of strange results (i can predict a bunch of Constructors running around wildly in the void!), including crashes to desktop, in fact.

Essentially, i guess, a setting option (similar to the Mine fields value, rare to abundant) which pulls these right off could represent a viable alternative; but, it ain't compiled into the code itself - as of now.

ad 1)

I think these geometric shapes are meant to represent and abstract real resources that CAN be mined. For example, the military resource actually may be an asteroid with important mineral ores or crystal deposits. The research resource may be some rare isotopes of an unknown substance.

But as there are an almost infinite possibility of what these resources could be, they all get abstracted as geometric shapes. In other words, it's just a matter of representation on the game map.

If you want to get rid of the floating resources in space you can just edit them out of ResourceTypes.xml. Make sure to back up files or use a mod folder though.