The saddle isn't too low. You want enough down angle from the saddle to the bridge (pin slots) to keep the strings from rattling across the saddle, and from the picture it looks like you have enough angle. As long as there is no string rattle you are fine.
EDIT: Since the question was clarified as to why the concern for the low saddle, I stand by my assessment. You have enough down angle after the saddle to transfer all the energy from the strings. You won't start changing tone until the strings are nearly flat, and even then there is tension at the peg down to the string ball that transfers energy into the bridge, so even if you were to remove the saddle completely you wouldn't have much difference in tone.
For an example, some Ukulele bridges have the strings come straight off of the wood, and the Cavaquinho often has the strings come straight off of the bridge knot.
I have on occasion deepened the saddle slot and lowered the facing wood of the bridge to allow a lower action, and the main issue is making sure there is enough downward tension on the saddle. In a few cases I've seen guitars where the bone saddle has been removed entirely and the strings resting on the wood of the bridge in order to lower the action and the guitars played just fine.