Regarding Franks understanding, there are three possibilities that I can see:
1) Frank never did the math. I am getting to around Franks age, and I have to pause and think when people ask me how old I am. If you asked me how long it's been since junior year of high school, I would need to pull out a calculator. Furthermore, what is 9 months before March? Frank is not an incest-obsessed weirdo, and his knowledge of his and Shannons HS romance does not solely consist of 'had a lot of sex ~9 months before Becca happened'
2) Frank did the math, but Shannon told him no at the beginning of their re-relationship. We know that Shannon is a liar, but Frank at the time did not, and likely would have preferred to accept it than sabotage his chance to get a mother for Abby. Wait for over a decade of source-amnesia to set in, and Frank might 'know' that Becca isn't his without ever re-examining why he thought so.
3) Frank knows, and doesn't have as much of a problem with it as he thinks he should. There are two reason that I think this. First, when Frank was negotiating with Becca, she points out the real reason Abby is off limits: Jess. Second, Probably the most meme phrase of Single Again is "We cant...You're my...". Searching through the script files for the phrase 'you're my' pops up a lot of hits for 'You're my father', 'You're my sister', 'You're my girl', 'You're my [character name]', etc., but the only time that phrase ends uncompleted and uninterrupted as in the meme, it is Frank talking to Becca. And when Frank does say that, Becca goes into reassuring mode about how it is alright for them to have a sexual relationship. Frank doesn't know that Becca knows, which is why he doesn't finish that phrase, and Becca knows that if Frank ever does then it will become orders of magnitude more difficult to continue sexing him. For comparison, when he talks to Lilly in similar situations his go to whinging is 'we can't...it's...'.