The old wisdom was to mount your VHF near the companionway so you could operate the coil-corded microphone while standing in the cockpit. Not so sure that is needed today, with all the other options. Most boats carry a handheld VHF as well as the mounted unit and use that in harbors, shipping lanes, etc. And since you seem like a technical person, Mads ... you can (apparently) train smartphones or tablets to work as cockpit repeaters for many of today's electronics, including AIS, GPS, chartplotters, depth, speed, and wind instruments.... Basically anything with a transponder or satellite signal can be trained to display on your handheld gadget. That carries its own frustrations & I don't think it is something I want for our boat. Tho my partner is clever that way & she can deal with that side of things. AIS, at any rate, can be easily split out to a number of displays.
Electronics are especially tricky because they don't live very long and get added or removed as options and needs change. It is easy for a nav station to become cluttered or haphazard with gizmos and wires running everywhere. One approach is to not cut holes in fixed panels for specific electronics, but rather to cut one large hole and attach a hinged or removable faceplate to it. Like TamTam shows, above. You can then alter or replace the faceplate as required, without leaving ragged holes in your lovely plywood.

Easy to get at the wires that way too, and you may be able to screw a plastic tub to the back of the area to keep water off your electronics.