The deployment finished finally with a total duration of 6 hours. In the log, there were about 25,000 warnings in total, all of them similar to the one in the question.
Can BizTalk even handle a large schema split into multiple files?
Despite warnings, the XML schema set seems to work without problems.
Is there any way to speed up deployment?
An obvious way is to remove any parts that are not required for the current usage. Actually, the current deployment only includes the PurchaseOrder noun (there are dozens of nouns in total). The actual problem seems to be the number of reusable components in OAGIS. They are located in a few files, but they are many. Removing any unused components would require editing the original schema files, which is not very practical.