DS already incorporated TSOP's work where it didn't directly conflict with the intent of the mod.
Examples of TSOP's work included would be reference fixes, typo corrections, textures all converted to dds format, etc.
Examples of TSOP's work not included would be any reduced texture/mesh that clearly takes away from the visual appeal of the game. Some necessities of the past like planets and trade ship textures, while they were included to help with the memory issue, in the future will probably not be included since they're not necessary reductions anymore.
The most recent updates to the core game that incorporated TSOP's work is just Stardock/Ironclad catching up to the rest of us, and as far as I've been able to tell, all of the files that were fixed in the core game are still necessary to be included into DS since there have been further modifications to them. I haven't gone through all of them, so I wouldn't doubt that there are probably a few in there, but that's just what I'm seeing so far.
As for the pirates, their system got an overhaul, so the odds are the DS pirates are going to need an overhaul as well. It's not the first time this has happened. DS pirates were modified in such a way that they became a viable force to have to be dealt with under the former system. Under the present system, those modifications are likely being amplified. More so since the computer players now participate in bid wars super funding the pirate faction. This is just a guess since I haven't had the time to sit down and look at them and digest the changes, but it's an educated guess none the less.
As for a weaker pirates mod, I think Ryat said he'd look into it after the official release of the patch and he had the time to sit down and look everything over. So I would expect something to happen to the pirates, either via a DS update, or at the very least a minimod update. Personally, I've always liked the powerful pirates, and the last time Stardock/Ironclad messed with the pirates they became damn near invincible pirates (which I'm still waiting for my copy of. ) with the powerful pirates minimod enabled.