How would I determine the ideal capacitor for a specific application
The two most critical parameters for a capacitor are capacitance, and voltage. 

As the BOM doesn't specify the voltage, it's possible that it's a low voltage application, and 'any' capacitor will do. 

A 100pF NPO in a 1206 (that's huge!) package, would be unlikely to be less than 50 or 100v operating voltage. The Johanson part you've identified is rated at 500v!

Most of the computing guts of an Amiga A4000 computer will be running at 5v and 12v, but it's possible there are higher voltage rails generated locally for non-volatile programming of stuff, perhaps 10s of volts, and this may be in that area. It might also be in the video display, where there are much higher voltages into the 100s and 1000s. 

I would like to think that for any voltage operation over the 'safe touch' voltage of about 50v, the BOM would specify voltage as a parameter. 

Small value ceramics (100pF is small), aren't readily available with less than a 50v rating, they are so cheap it's just not worth the manufacturers bothering to hold multiple lines with some cost reduced by requiring a lower voltage.

You need to find out the voltage that the part will be subject to in operation. Once you've done that, just pick the cheapest 100pF NPO capacitor that exceeds the operating voltage by a factor of 2 or more, subject to stock and delivery. Johanson is a premium RF brand, as you can tell from the price. There's no need for that, unless you need the voltage, or the RF qualities.

Caution, when you're looking for 'large' value ceramics, 1uF and above, then it's a whole different ballgame, played in a minefield, and all the reassuring noises above are irrelevant.