Last year I got a Schengen visa through the French embassy due to being married to a British national. I am South African. In the end we couldn't afford to go to France but went to Portugal instead as we had free accommodation. So I didn't enter France at all. Will this affect me getting a Schengen visa again this year and can I use the French Embassy again as this is the quickest route (no supporting docs needed except marriage cert. and husband's passport)?
The rules should be the same no matter where you apply. The fact that you did not need anything else than the marriage certificate is unrelated to the fact you applied from the French consulate. In your situation, any consulate from a Schengen country should deliver a visa quickly and free of charge if you are traveling with your EU-citizen spouse.
Since there are no systematic checks at internal borders within the Schengen area, neither the French consulate nor any other Schengen country have any easy means to check if you did in the end go to France (although they might see the entry and exit stamps and inquire about it I guess) but you should still apply to the country that will be your main destination. Except if you really want to go to France this time, the French consulate should decline to process your application. It would seem relatively easy to get away with lying about it since you don't need to provide any documentation but it still seems like a bad idea.
Incidentally, since you have a right to visit or even move to any other EU country together with your husband and you already used a Schengen visa correctly (i.e. did not abuse it to immigrate illegally), getting a new one should be no problem at all.
No, it makes no difference. Only your port of entry is tracked: since there are no more border controls within Schengen, the EU has no way of knowing where you went after arrival.
Update: However, you are supposed to apply at the embassy for the country where you spend the most time. If that's France, great; if not, you might be better off applying elsewhere.