While I can understand why spamassassin has a limit on the size of messages that it will process, I think there is a reasonable middle-ground between scan and don't scan in the case of such messages.

Since such large messages are usually due to large attachments, such as zip files, or graphic (i.e. JPEG, etc.) images, why not process the message but just skip the large attachments?

There is a lot (i.e. in headers, etc.) that can indicate that a message is spam without even looking at the attachment, or even just looking at the attachment's headers but without running the content through the expensive scanning process.