You can increase the font size which will make the boxes bigger.  Also, you might like the new inlet/outlet highlighting that's in Pd-extended 0.43 and pd-l2ork.  The inlets and outlets are tagged using Tk tags, so you should be able to change their size using the Tk canvas commands 'coords' or 'itemconfigure -width', etc.  I've never tried tho.

Their hitboxes aren't though - canvas_doclick in g_editor.c has hard-coded numbers.

Arg, yes, that's true... sigh...  but I find the inlet/outlet highlighting helps a lot.