Low voltage DC Supercap UPS Design
Your first schematic is pretty straightforward to make, and will most probably work fine. The decrease in efficiency is not that important when you're running on mains power. The second one will be trickier to implement.

For either design, you won't be able to use the cheapest boost converters available, because the most widespread are made for the Li-Ion voltage ranges (i.e. they boost 3..5V to 5V).

Also keep in mind that capacity does not measure the amount of energy stored, that would be C*V2, so a 10F capacitor rated at 2.5 volts stores the same amount of energy as 2.5F capacitor rated at 5V or 0,1F capacitor rated at 25V. This fact also explains why low-voltage caps are cheaper and smaller.

Yet another issue with supercaps is that they often are just gloryfied RTC backup batteries with recommended discarge currents of order of 1-10 mA and internal resistance of 1-10 Ohm. Pulling 0.5 A from such caps will result in permanent damage. Carefully read the whole spec before buying, don't just check capacity and voltage and assume everything else will be fine.

I still suggest you consider a Li-ion battery as the cheapest and most effective solution. That's what I use in my Banana Pi, which exposes Li-Ion battery pads on the board and requires no extra parts (besides the battery itself) to have back-up power.