You can get a pod filter to fit over the velocity stack. It is less efficient, however.
The rubber boots won't do anything to help performance other than make the intake resistance-free (which only improves the performance with a lot of other changes to tune the bike properly). A velocity stack is a precision piece of tuning that gives the bike forced induction for a very narrow portion of the power band. Basically, they prevent the shock bubble from the intake valves from escaping, so that it returns to the valve just as the valve is opening again, forcing extra air inside. It's a sweet bit of precision tuning, if it is done properly.
Performance by what definition? Maximum power? At what throttle setting? For how long?
Velocity stacks were/are quite popular in the drag racing or land speed record arenas. I can't think of anywhere they were used with success in a duration event.
The funnel does a small bit of compressing the air, using the mass and velocity of the air at higher speeds. Also, part of what a velocity stack does is help keep the intake airflow laminar, as in non-turbulent. This is something most pod filters ignore. Anyway, turbulent flow is bad because the eddies cause higher and low pressure areas in the intake runner tract. The positions of these pressure differences vary along the tract with the air speed. When these pressure differences extend over the fuel exits into the carb bore, it can upset the flow of fuel into the carb bore, making some RPMs richer and other leaner, even though mechanical mixture ratio settings were maintained. A velocity stack can only do the job properly if it's mouth is completly unobstructed. A filter or screen at its mouth will certainly turbulate the airflow and negate much of its beneficial effects.
I'm curious as to just how the "shock bubble" is kept from escaping? In a tuned exhaust pipe for two 2 strokes, there is a reverse cone to reflect a pressure wave back toward the combustion chamber. A velocity stack has no means of reversing any shock waves. There is only the atmospheric pressure at the mouth of the stack, assuming the carb slides are wide open.
While I don't think the rubber funnels in the stock air box are tuned for a specific RPM or RPM band, they do help with the laminar flow through the carb bore and in keeping fuel flow predictable throughout each throttle setting. The turbulence from the air filter is well ahead of these rubber cones.
As to the topic title, I vote for engine death. Just about anything that makes an engine produce more power will increase wear and shorten it's maximum life. But, when you add dust and dirt particles blasting onto the cylinder walls during combustion, it's certainly going to errode those walls faster than with clean air. It's a classic trade off; power/durability/longevity. But, then, I feel I've already shortened the life of my engine by using the foam Uni filter in place of the stock paper type that blocks smaller abrasive particles.
Don't know how I sleep at night...
