I don't know the answer but perhaps other peeps more familiar with database sever issues can weigh in.
If it were my issue, I'd ask my server "gods" to check how the server database is working, if any issues.
Ignore this comment at will. I am not a power-user, but have used WA extensions for decades. I suspect it is a server issue, not a WA issue, but as I said, others here can help more than I can.
I have had huge shopping carts in the past with thousands of products and haven't had an issue.
Let us know what you find out and share with the community.