While I agree that there does not NEED to be a warning as there is plenty of ways to work around it, it would be nice if one was added.
I think instead of adding a warning, a representation in hyperspace, perhaps in the neutron star gravity well "jump" point would be better. Or maybe add it as something that shows up when using the neutrino detector around the jump point, making it glow white or something (I.e. the pulsar beam is leaking through and the neutrino detector picks it up) when the beam overlaps.
The problem with a jump warning is the game pauses. In the case of hostile fleets, in many cases, just waiting and clicking again isn't going to make them go away. It's really a one time warning you want, so having it as a text as you're about to enter is fine.
However, if you intend to enter a neutron star system, and don't actually use one of the ways to mitigate the danger on enter that already exist, then the gameplay loop with the neutron star is click on the jump point, pause game with text warning, click don't jump, wait some guessed amount of time, click on the jump point, pause game with text warning, click don't jump, wait, etc. It's entirely possible if you wait the wrong amount of time, to miss the opening and get the opposite beam, or alternatively you click too often and now you've clicked 10 or more times just to enter one system safely. The game flow is just kind of terrible.
A less elegant option than displaying the information live on the hyperspace map about where the beams are would be to tell you the number of estimated days until the beam no longer overlaps in the text warning.