There is no observed solid surface to Jupiter, and by mass it's something like 75% hydrogen, 25% helium, with some other stuff thrown in. To understand how something like Shoemaker-Levy 9 can still "Hit" the planet, remember that gases are still matter, and don't like to be moved around.
For a more everyday experience to compare it to, take a look at a basin of water. You can slosh it around, fill things, submerge things, and it offers little resistance. Now, slap it with an open palm (or do a belly flop) and tell me you didn't hit anything!
If you go fast enough anything will hit back hard. Shoemaker-Levy 9, or any object, falling into Jupiters atmosphere will hit lots of air, be slowed, heated, and if it hits a particularly dense pocket may even explode due to the pressure & shockwaves.
Another example that applies here is supersonic aircraft. For an airplane that isn't designed correctly, going faster than sound is very dangerous as the pressure waves can rip the airframe apart. A cometary impact in an atmosphere is easily going 10 or 20x the speed of sound, and isn't really designed for it. The object will burn, scatter, and disintegrate.
The reason we could see the effects: The comet dumped massive amounts of energy into the atmosphere of jupiter, akin to many large nuclear blasts (how many I don't recall). Each spot you saw was easily comparable in size to that of the entire EARTH!