I don't think so. We see them use two Seagulls, one that's destroyed at Enceladus and the second one which they use to dispense sonobuoys in Episode 13 against the UX-01 and in Episode 16 at Beemerra before it is finally destroyed by "friendly" fire on Leptopoda (Prison Planet 17) in Episode 21. After that we never see the Seagull again, so it's safe to say those were the only two that were aboard.
We have confirmation in Episode 17 that there is a matching starboard hangar (we see them bring Type-100 #04 to the hangar deck with the starboard wing facing outboard, and then the next scene sees the Type 100 flying from the starboard side of Yamato), so probably I'd say the second Seagull was initially in the starboard bay. My guess is they only did CG animation of the port side hangar to cut down on production costs, so at some point we have to assume they moved it to the port side for some reason (and then had it back in the starboard side when Melda's Czvarke was taken aboard in Episode 10). The dust-jacket of the Garmillas design book also shows this hangar with a Seagull in it, albeit at different scale compared to what we see animated.
The Earth design book has coverage of the design on pages 94-97 for the blister hangars. They show the possibility that two Type-100s could be stored in each hangar (one above the other, probably forward of the main hangar door). Through Episode 21, we see only the one Type-100 in the hangar bay at one time though. I'd say each hangar bay had two Type-100's (for a total of four, hence ship #4) and one SC-97 Seagull (for a total of two).
The hangar bay is about 26 metres long and going by one detail drawing on p96 is 16m wide with the control area, platform, and storage area covering 7m of that. The bulbous part which protrudes from the main hull is thus 9 metres wide and the illustration shows has an 8-metre height clearance.
The assault transport in Yamato 2 Episode 13, looks to be considerably bulkier. I'd be worried about both its height and its width as far as fitting into the Seagull hangar goes, the Seagull itself is a tight squeeze. To top that off, there's the question of the nose loading ramp. They'd have to engineer a different boarding gantry, especially if they were loading heavy equipment aboard. Overall though, I think that they'll have to find somewhere else to launch it from.