I have already noticed that Shopify bulk operation has an issue with orders with many line items. The only workaround I have found that works, is to use non-bulk queries.
What I do is if I my bulk operation returns with an InternalServerError, I retry the query non-bulk. Of course this defeats the purpose of bulk operations, and requires me to maintain a whole bunch of extra code, but until Shopify fixes this, I have no other option.
I agree that this is unacceptable from Shopify’s part, this should be fixed.