1. Will the switch and/or fuse also take away current resulting in less brightness?
2. Would the ohme value of the resistors need to be adjusted taking point 1 into account?
3. What would be the recommended fuse in terms of holding current and trip limit?
4. Are there any other things that need to be accounted for?
1 No
2 No
3 1A, smallest value you are likely to find, not really needed with a PP3 supplying the current.
4a Unless it is a very large boat with long wiring runs, the thinnest wire you can find will be fine
4b If using a PP3, a fuse will probably not be needed, the battery will provide its own current limiting.
4c Different colour LEDs have different efficiencies, yellow need nore current than red or green, their resistor value will therefore need to be different. Using red and green, typical Vf and If would be 1.9V and 10mA, adjusted by fitting appropriate resistors and reducing the total current. See 4e.
4d LEDs are pre-coloured unless you get white ones. White are the least efficient.
4e The switch shown "should" be OK, but might be a bit near its limit for 100mA. If a specification is available, that should help.
A lot of models have eye wateringly bright nav lights. On real ships and boats, they are usually just above the legal minimum required. Deck lights are much brighter.