They're cannonical alright...

DQM1 takes place in the Heaven trilogy (IV-VI), specifically featuring Terry and Mileyu from DQVI as the main characters (albeit younger versions of them). DQM2 supposedly also takes place during the Heaven series, though I'm unclear as to how it fits in.

There was a third DQM game released for the GBA called DQM Caravan Hearts, but it was never released in the US because... Well... Square-Enix doesn't care about DQ in the US, and the game was released in Japan right before the merger. It features Keifer from DQVII, but he gets transported to the world of DQII, so it ambivalently fits into both the Roto trilogy (I-III) and the current unnamed trilogy (VII-IX). I can't tell you more about it than that.

The assumption is that the games officially happened in the timeline of the series.