Buddy, yes you can see the Top Hats from the Engine Bay. They serve their purpose plus also add a nice bling to the Engine Bay. I have them
The purpose behind the Top Hats is to allow more Shock Travel (just like when you Preload a Full Coilover Setup), so you can be tucking tire and not bottom out like you would with out them. Extended Shock Travel + No Bottoming Out = Longer Shock Life. If you have a lowered car, I'd suggest picking up a set of the GC Top Hats (at least for the front, not really needed in the Rear). Ground Control Top Hats also helps align the lower control arm up so that the suspension geometry is more even. Just my
Stock Shocks are not meant for Lowering a vehicle as you mentioned, that's why they are "Stock". You need Aftermarket Shocks. I personally run this setup: Koni Sports "Yellow" Shocks, Ground Control Sleeve Coilovers (Custom Spring Rates), and 4 Ground Control Top Hats. I love it, I can adjust height as well as damping. I have other Suspension items (Swaybars, Strut bars, Cross bars, etc) that also help as well in the performance and handling of the car.