When I did similar things I always symlinked the top folder of all PDFs to the vault, never brought the physical pdfs into the vault as syncing the vault would have been impossible after.
I remember little freezes but even on a smaller laptop 30k+ files were indexed.
I reckon there is some issue with one particular path (folder) or file.
But I would NOT recommend going down this route at all.
Add all your pdfs to Zotero, it will index all your files and run LLM models on the txt files, which you can turn into md files as well with Python or whatever. You can use other software like CursorAI for this (import workspace with your indexed files: NOT PDFs, but raw txt/md).
You do NOT want to use Obsidian for all things.
Alternatively, use Cursor AI to regex search your stuff for common topics and only pick those index files or pdfs to add to Obsidian, to a dedicated project vault.
I am currently trying out Neural Composer for a smaller batch of books (md-index files because I have them, but I could try original PDFs) to see what gives.