Moving things with the harpoon doesn't have nearly as much to do with mass as it does with thrust since everything is suspended in air.
Speaking from the perspective and recollection of the former glorious harpoon, it was always good on the front gun of a Junker and rear gun of a Squid and of course excellent on a Galleon. Should the armor piercing modifier be properly buffed putting one on the front of the Pyra should yield excellent results as it reels you slowly into its mortar with repeated harpoon shots. It should also be quite good on a mobula, which if you look at the stats, isn't nearly as fragile as people think (though it really does hate rams, vertical acceleration usually makes them a non issue though).
Well, if we are gonna talk physics, air resistance does take mass and profile size into account since into the atmosphere the heavier object will fall faster and/or requires more intial power to move, so it does matter a whole deal here unless GoI uses vacuum physics and I don't know of it.
Of course the Squid would be able to drag the Galleon, but it would take time for that to happen and the Galleon has engines of its own, which are much more powerful than the Squid's and this is all time you spend while they take aim at your rear.
I don't exactly get the Pyra example, are you saying you would use the harpoon as an armor piercer? if that is the case and my answer is simply 'no' that is not possible with the fire rate and the damage it deals and there would be no reason for it to deal any more anyway.
Old harpoon might have been good, but as I posted airlier, realy shows why this gun has issues in general, it restricts horizontal movement and has no counter, plus the only ship that could take real advnatage of it is a Galleon, MAYBE a Junker on its side with a frontal gun that can form a bi-fecta with the other side gun (talking about a new harpoon btw, not the old one, that's as gone as the old Flak is). Anything else would either lose too much firepower or be forced to face the wrong direction due to harpoon physics that force turning.
I'm certain we both agree that the Harpoon should not be a damage dealer, even less an armor shredder.