A shaker motor is exactly that - a compact motor with little weights which spins & shakes the machine (making a small noise). It sits inside the coin door to the left, near the tilt bob. Modern Sterns are programmed to use the Shaker but they're optional extras in most cases. I have 1 in my Spiderman and think it's great! You'd need to put some damping around the backglass and playfield glass to stop annoying rattles though.
That Flipper Fidelity speaker kit is 2 backbox speakers and a beefier cabinet subwoofer - they replace your 3 existing/factory speakers. If it's loud enough you might get some vibrations, but more likely a better quality sound and much more bass. I know some people prefer to just add an external powered subwoofer in addition to the 3 factory supplied speakers to improve the bass - can't comment on that myself as never tried it; prefer to have it all built in where possible. Also have the FF speakers you link to in Spiderman. Sounds awesome at higher volumes.
Both are great upgrades. I'm not sure which i'd choose to be honest. Maybe the Shaker as it adds an extra dimension to the game, whereas the Speakers just make the sound better...
Does that help?