Mark Steinberger writes:
 > I've noticed that inclusion of hypertex \specials can affect vertical
 > space. E.g., including the \specials immediately before an equation
 > environment sometimes adds space above the environment.

ah, I know it well

 > Can latex address this issue, or is it an underlying tex problem?
 >
 > Has anyone else noticed this? Is there any potential cure?

LaTeX can and will address this problem, but it will require some work
on hyperref and other macro packages to interact with what They do. So
don't expect it very soon. Basically, it involves delaying the
addition of vertical space to a point where the \specials stop
interfering. David and Frank can explain better, but the bottom line
is that a solution is on its way.

Sebastian