For consistency with the standard text region and for usability within interactive handbooks, I propose changes:
If a hyperlink with file target in a text region is Ctrl-clicked, then the target is opened in a new SMath instance. Recently, SMath switched to pre-loading the plugins, this practically prevents fast browsing through interlinked SMath documents (like the interactive handbook). The proposal is to make the behaviour consistent to the standard text region, where the document is replaced by the link target, which is fast and convenient (and safe, due to the check for changes).
Also, please make relative file paths relative to the document directory, not to the current directory (otherwise documents with relative links would need a mandatory CurrentDirectory(DocumentDirectory()) statement.