Molly is a good parent, no matter what anybody says, no matter what her twin boys get up to in the night she is, really. She isn't blind though, she isn't deaf, she knows what the bangs that come from Fred and George's room really are. She's not dumb, she invented that spell, with her brothers of course, it replaces sexual sounds with bangs and booms.
Yes, she made that spell with her brothers because they did need that spell, that's probably how Fred and George came across that spell, Gideon and Fabian were still together after Molly got married. They probably saw them one night, and 'helped them out' by giving them the spell.
Molly is a good parent, she doesn't judge, she doesn't talk about it, she doesn't tell anybody, because she knows that one day, this will all stop and they will go their separate ways, each marrying a different girl. That's what Molly did, she separated from Gideon and Fabian, she married Arthur.
She only thinks though, she doesn't know if Ginny is involved, but she can't be sure, especially since Fred and George were much better at hiding it than Molly was with her brothers. She couldn't know if they were alone, or if they had someone else with them.
Molly is a great parent, because she knows the happiness that this love will bring them, and she doesn't tell anyone, she won't ruin it for them, she doesn't judge, she doesn't stop it. She doesn't think that it's wrong because she has felt this love, this special close love.
Molly is the perfect parent. And all her sons thank her for never telling anyone.