A box contains:
a) wires of different sizes (for example #12 which requires 28.7 ml and #8, which requires 45.1 ml), and
b) a couple pairs of wire connectors, and
c) a flush mounted device of less than 2.54 cm,.

The #12 wires are connected to the #8 wires and the device is connected to a circuit with tails of #14 wire, which require 24.6 ml each, but aren't counted because they don't leave the box.

When I deduct the number of wire allowed in the box for wire connectors, can I reduce the number of #12 wires allowed? If the code doesn't specify, it must be my choice.

Can I deduct the #14 wire from the allowable fill, because the device is connected by that size of wire?

Only makes sense that the biggest wire be deducted. You have to use a bigger wire nut on bigger wire which takes up more space in the box.

Same wire nut:

http://www.idealindustries.com/products/wire_termination/twist-on/b-twist.jsp