Actually, when applied to a stock length shock, those top hats DO have a purpose.... but for a setup like that, where you can adjust the height of the shock body in the fork, it means a bit less.
Shocks will ALWAYS function beter within a certain range of movement... i.e. if you SLAM your car, and the piston is at the bottom of the shock body, it won't perform nearly as well as it would if it was closer to the middle opf the shock body with proper oil above and below the piston.
SO, using the top hat allows you to raise the piston in the shock body by an inch or so, which is enough to allow the shock to operate in much more ideal circumstances.
I've seen this proven on a shock dyno on racing shocks, and had this discussion with the guys at Penske and Strange when i was working out the suspension on my race car... they HAD to know what the 'installed height' of the setup would be so that they could give the piston adequate clearance above and below by having the correct shaft length.
That top hat is a band-aid of course. You can send your Koni shocks in for instance, and have them shorten the shafts and bodies so the shocks are 'optimal' when the vehicle is lowered really far. This is usually what the guys who auto-cross and road race do.