From the Tau Empire codex, page 123 (emphasis added):
Pinpoint: All models firing at the target as part of this shooting attack gain a bonus to their Ballistic Skill for the duration of the shooting attack.
The increase in BS or Ignores Cover affects the model doing the firing (Scour has similar wording to the above). This is not a complication with Target Lock or Split Fire models, since they still have to fire all their weapons at a single target. It is an issue for Gargantuan creatures, however.
Let's say an Imperial Knight has 5 markerlight tokens, and a unit of Space Marines with no markerlights is also in range. The Stormsurge takes 3 tokens on the Knight for Pinpoint, and 2 for Scour. It then fires the Pulsecannon at the Knight and all other weapons at the Marines. In addition to the affects on the Knight, the Stormsurge still gets +3BS and Ignores Cover against the Marines.
Silly? Yes. But it is Rule as Written.
This is a double-edge sword, however, when we look at the Stormsurge's rules for Stabilizing Anchors (Tau Empire codex, page 104, emphasis added):
In the Shooting phase of your next turn, and in each subsequent Shooting phase, a Stormsurge with its anchors deployed can fire twice. Make the second shooting attack directly after the first has been resolved.
The wording of Pinpoint and Scour only affect the current shooting attack, but with anchors, the Stormsurge is considered to be making a second, separate shooting attack. That means the BS increase and Ignores Cover does not carry over into the second attack.