When grinding AI3, is it better to use a deck which:
has a high win chance, but low to zero chance to EM
OR
has a moderate win chance, but when it wins, it has a high chance to EM
Option 3: fast.
EM is almost irrelevant to AI3 (unless you're grinding for score), as most of the money from AI3 comes from the cards you win in the spins, and any unupped AI3 EM decks are slow, unreliable, or both.
What you want to do is find whatever deck gives you the
most wins in X amount of time, so you pretty much need to look at both win rate and TTW.
For unupped AI3 grinding for money, in nearly all cases the best option is to make the fastest rush you can come up with without giving any thought whatsoever to defense. Not very many of the AI3 decks can move very fast, and if your rush winds up against a deck that puts out good enough defense to shut it down, you just lose/quit and move on to the next one. This broad strategy tends to produce the most money from AI3 unupped.
Of the two options you mentioned, I'd probably personally choose high win rate and low EM rate over high EM rate and mediocre win rate, since as I mentioned above, EM in AI3 is not a big concern unless you're score grinding.