volt management for a big circuits (mother board if you will)
1) Yes, generally speaking it should be fine to send the 5V to the arduinos and netduino, unless any of them have ADCs or DACs that you intend to use and that are sensitive to voltage source fluctuations. Note that in any case you should include a capacitor at the voltage input pin to each chip. Use wires/traces that are thick enough to transfer the current that you need, and best not to put the chips in series along a single power line (unless the power line is sufficiently large to minimize the voltage drop along it.

2) I've only ever needed to put a single fuse at the input of the entire circuit board. I wouldn't expect any average use-case to need more fuses than that unless you're worried about some IC drawing too much current or feeding the power supply to a daughter board.

3) Correct, as long as you keep the current below what your voltage regulator is rated for. Note that if you are drawing 5A and plan to use the 7805, then you're going to burn (12V - 5V) * (5A) = 35W just in the regulator. You'll need a beefy heat sink. A switching DC-DC converter might be better for this case.