Although I think that is not documented anywhere (we will fix that), toolbar icons should always be squared and try to have the same size as the ones provided by Cytoscape (32x32 px).
We fixed that in 3.6 by limiting their width/height to the max allowed, because the available toolbar space is limited and has to be shared by many apps. Too many icons or unnecessary ones (e.g. help, info) can easily clutter it and make it look more complex to the end user.