To put it into perspective, the speed of sound (mach 1) at sea level is 340.3 meters/second. Mach 5, therefore is 5 * 340.3 m/s = 1621.5 m/s. In a three second Shadowrun combat round, the hypothetical hypersonic penetrator we are speaking of travels 4,884.5 meters. Honestly, at extreme sniper ranges, there would be some time between the trigger pull and the impact upon the target, since bullets tend to travel around the mach 2 mark (and thus travelling 680 meters/second or so). Modelling this in game would probably complicate things a bit, so I wouldn't recommend it.
Assuming a heavy MP laser is used for anti-missile defense (which is about the right size) means that, at extreme range, the laser's targetting system must lock onto and maintain lock, and must traverse the laser aperature onto the projectile, in less than one second from the time it hits effective firing range before it strikes the host vessel. From aquisition, to traverse, to firing, to holding onto target in order to deposit enough energy to disrupt a solid slug of dense, armor-piercing material in less than one second. Although it might be possible, I find it highly unlikely (too much is going against it).
EDIT: Spelling.