It is currently possible to break through JP blockades with ease because
the Fire at Will command negates jump shock almost entirely. Not only it makes it much easier to assault JPs with regular mass squadron jumps (
spoilers,
also spoilers) or even squadron-capable missile boxes, but even standard-jumping a blob of fighters would be a valid tactic, as they'd experience minimal, if any, delay. I consider this to be a pretty serious bug and really hope it gets fixed in the next version, but if you're unwilling to abuse it now, consider high-jump range jump-capable fighters to lead the blockading ships away from the JP before sending in your main force, this works really well if your enemy doesn't have AMMs
(spoilers again)As I understand it, firing at a waypoint isn't going to be affected by jump shock.
Honestly, this feels like a variation of the same bug to me (waypoint targeting ignoring jump shock same way fire at will does), but also waypoint-fired missiles are in a pretty weird spot right now. As in, the only way to make them switch targets from a waypoint to an enemy ship on the fly (that I've found) is to use the currently bugged Move Waypoint command while the missile is in flight, which makes the missile switch targets using its on-board sensors. This can only be done once per game launch (need to save/close/reopen before moving a waypoint again) and there's no telling whether this will work once waypoint moving is fixed in 2.6.0. It would be nice for missiles to use their sensors to target anything in range without the need for waypoint shuffling, but on the other hand, being able to fire at targets without the need for active sensors or an appropriate MFC just by applying a little bit of math (not even always necessary) might be a bit OP.