Win32::API::Prototype and Win32::API::Import effectively do the same thing. They both export a sub into the callers name space that does:

sub ApiName {
    return $globalHash{ 'ApiName' }->Call( @_ );
}
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The name of the global hash is different between the two packages, but the performance should be close to identical.

You will get a minor performance gain by avoiding the import sub. Ie:

usw Win32::API;

my $api = Win32::API->new( 'dll', 'api', 'II', 'I' ) or die $^E;

$api->Call( @_ );
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You avoid an extra level of perl subroutine call and a hash lookup. For all but the lowest cost APIs, the difference will be minimal, as most of the cost is in converting the call parameters to their C equivalents before calling into the DLL. It might make some perceptible difference for calls that take no perameters.

If performance is a realistic consideration, you'd be better off writing Inline::C wrappers for the APIs you need.