Starting with v10 and on v10.0.1, xpage resource aggregation throws error 404 if it is referencing an invalid or nonexistent js library. This was not the case in Domino 9 versions.
However, apparently this is a security enhancement implemented for v10 releases since silently ignoring an invalid/non existent js is not correct as per the AppScan vulnerability scan tool - this is a tool that has been used to scan sample applications created using XPages. This tool was a requirement for adding the XPages app to IBM Bluemix (which is a cloud platform) and these fixes were done in V10 releases (to support Bluemix requirements). Regardless if the Xpage app is on IBM Bluemix or not, the XPages runtime needed to conform to the Bluemix requirements thus v10 code complied to this requirement.
Request that in v10 instead of generating a global 404 during aggregation, signal the lack of a resource somewhere else/differently.