I'm sure one of the DL regulars will be able to answer more accurately, but I think as it is so much more compact than WDW there aren't really what I would call any 'secret" paths - but there are a few "less-used" shortcuts that we enjoyed discovering.
You can cut through from Fantasyland to Tomorrowland via the archway just to the left of the gateway of the castle - it takes you past the wishing well and Snow White's grotto, which is always a peaceful little spot.
On the other side of Fantasyland there's the Big Thunder Ranch Trail (I think that's the name?) that starts by the Village Haus restaurant - its a pretty major thoroughfare but it often is quieter than the main route from Fantasland to Frontierland, and it takes you around the back of BTMR which is fun.
And there's always the shortcut by the toilets opposite the Tiki Room, which cuts through to Frontierland.
I wouldn't class any of them as "secret' but they're fun to discover none the less.