Are advertisements allowed for submitable run ?

Advertisements are not a problem, so you can submit a run with them. Just calculate the real time, considering the ads. Leave the in-game time unchanged.

I don't really understand the rules with duet speedrun timer for mobile versions. And is the audio required ?

In Duet speedrun mode, there is an in-game timer that determines the time. In most cases we make the real time same as the in-game time, but in some cases we change it. In general, this is not necessary, because the time of the run is determined solely by the in-game timer.

Audio is not required

Or you can turn off your internet connection, i think the ads won't show up if you do that!