Going to go out on a limb here and say "probably".

The reason for the high potency of some moves is due to the time it takes to perform the Sanji-in (Three seals/mudras). While +20% extra damage from Kiss of the Viper/Wasp may seem incredibly good in conjunction with these kinds of potency around 200-400, and Huton (Wind) granting +15% attack speed for 70 seconds (which is insane on its own), it likely is to compensate for the loss of dps while performing the actual Sanji-in. It may not look like much, but every second lost not doing damage, is just that, loss in damage, but I think that there won't be no bigger problem catching up, at least not while Huton is active.

While MNK is dependent on Greased Lightning III to keep damage going, and indeed can be troublesome to keep up, I suspect that at least in the end, NIN will be slightly stronger. The insanity that is Trick Attack (+10% damage taken by target for 10 seconds) is enough to grant a spot to a Ninja in any party.

I think a big part of using In, like Doton, Katon, Huton and Raiton is dependent on whether doing one while another is active, erases the currently used In. IF that is the case, and IF Huton is canceled when performing for example Raiton, then it would be extremely vital for the Ninja to quickly get Huton back up FAST again as every second lost with the 15% attack speed buff up will likely get it below MNK.

That's about all I can speculate about at the moment. As a main Pugilist/Monk myself, I am very curious as to what skills we will inherit from Ninja, and vice versa.
I do however think that an incredibly skilled Ninja will do more damage than an incredibly skilled Monk. /grovel