Where do all the NAD+s come from?
There is of course a pathway that synthesizes NAD+ de novo, usually from tryptophan, aspartic acid  or vitamin B3, or salvaged from compounds like nicotinic acid, nicotinamide. You can read more about it here: https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide#De_novo_production
The fact that TCA works in isolated mitochondria is not necessarily the effect of de novo synthesis. The reason for that is the cycle-like fashion of NADH production in the TCA and consumption of that NADH for electron-chain reactions (which recreate NAD+) or other reactions involving oxidoreductases. Redox reactions do not change the overall amount of the coenzyme. But in a living cell, some reactions will irreversibly consume NAD+, ADP-rybosylation may be an example. Still, the cell prefers the salvage pathway over amino acid pathway, because it consumes way less energy.
ADP and NAD+ cannot pass through the membranes without channels. Both are polar molecules and only non-polar molecules such as steroids can freely pass through the cellular membrane without any help from transport proteins.