Very unlikely. We only know about one date which didn't even end well:
Doofenshmirtz then tells him about one of his first dates. It was with Linda Flynn and they were in a drive-in theater, going to watch a film. Linda says that she would like to be a pop star one day. Doofenshmirtz sarcastically replies that he will take over the world, and she suggests that he should start small and try to take over the Tri-State Area. Doofenshmirtz says it's unlikely but he'll try. He then brings out a machine to make the movie's sound 5th Dimensional and attaches it to their car. Unfortunately, the machine makes the cinema screen explode and blast off into the sky. Whilst finishing his flashback, Doofenshmirtz trips on one of his traps and knocks his latest machine into the Flynn-Fletcher house in the front lawn. - phineasandferb.wikia.com
I don't think in one date he can father two children and it didn't even end well. From wikipedia:
Phineas's birth father is never present or discussed in the series, something Marsh and Povenmire have stated that they fully intend to keep that way.
Same applies for Ferb's mother too. We don't know. Fans can make any theory, but the creators want to keep it in suspense.
And many sources/people (1, 2) claim that creators have denied this theory.