Part of the problem might be the sheer size of the models, e.g. the UCS Star Destroyer will have thousands of pieces and the mesh data will be extensive.

Materials and meshes with zero users are automatically deleted by Blender when the file is saved (unless you have set a special flag to force them to be saved). So, if you're faced with duplicate materials like mb😒olid.21, mb😒olid.21.001, mb😒olid.21.002, etc., just update the meshes that have these materials so that they all use (say) mb😒olid.21, and then click save, the duplicates will be erased.

I did write a python script about a year ago that can be run inside Blender and should erase all duplicate materials and meshes. I am not sure if it will still work given recent updates to mecabricks materials, but it might be worth trying.
https://www.mecabricks.com/en/forum/topic/1541/1
MAKE A BACKUP of your Blender file BEFORE you run the python script!!!

Edit: Oh, one other option - in the Mecabricks workshop, import all of your models and then export a zmbx file containing everything. On import to Blender, there will be no duplicate meshes/materials, and you can manually separate each model into separate objects for animation.

Nice one thanks! I hadn't thought about putting them all together first before export! I did try your script before this post it seems in 2.9 it doesn't work, whether its due to blender or mecabricks I'm not sure.

Thanks for the tips!

For information, I just had a chance to look over my python script again. I'm not sure why it wasn't working for you, but I noticed that the mecabricks meshes and materials are using a new naming scheme, so I updated the script to run again. I've only tested in Blender 2.83, I'm not experimenting with the 2.9 series as I need some consistency for my current projects.

Using a test model, importing it once generated a 59.4Mb file, importing it twice generated a 105Mb file, and running the script reduced the size from 105Mb down to 67.5Mb. Just remember that running the script only reassigns materials and meshes - the duplicates remain loaded in Blender but are classed as "orphan data" since they are not actually used in any scene. You need to save the Blender file, close it, and reload it for the orphan data to be completely erased.

hi! mecabricks now auto links the materials and stuff. except for importing models another time.

@Citrine Really, it can do that?? Wow, Mecabricks never ceases to amaze!!