When saving a page containing graphs in VE, any booleans set to true in graph specs will show up as either "" or null in mw.config.wgGraphSpecs, causing the graph to not render properly. Once you refresh the page though, booleans are fine.
Is this bug still happening? I don't see it -- I just went to https://www.mediawiki.org/w/index.php?title=Extension:Graph/dimpvis&action=edit and clicked "preview". After which, in the debugger, I highlighted the graph and copied the graph id from two levels up (for me it was c5f25fc7d889ecbf3e269db910893a93170d04ae ).
Afterwards, in the debugger I ran JSON.stringify(mw.config.get('wgGraphSpecs')['c5f25fc7d889ecbf3e269db910893a93170d04ae']) from the console - and I see that the graph contains both :true and :false, meaning that bools preserved ok.