1. If the defender uses missiles bring ONLY ships with CIWS. These can defend themselves against missiles to some extend. Ships with other forms of missile defenses are undefended and get all the good news.
Based on my own experience I am fairly sure that beam PD will work just fine, since jump shock is implemented essentially as a crew Reaction penalty which does not affect PD. At least, the last time my railgun fleet assaulted a jump point PD was not a problem for me. I am not sure if AMMs would work the same way, but they are bad for JP assaults anyways as you rarely have the necessary distance to make use of them. CIWS is bad as it only protects a single ship and is nearly useless for even a 3-4 ship jump squadron.
Generally for a specialized warp assault fleet, you want ships with extra armor - not shields, as these will not be as efficient in terms of protection per HS. Possibly for a sufficiently large ship shields may be effective due to the randomness of armor damage but generally, you will make one assault and then send the fleet back for repairs so you should prioritize tactical efficiency and accept the higher repair costs. Otherwise, you want to use high-power beam weapons at close range - plasma and railguns are effective here, lasers will also be fine, particle lances will give a powerful alpha strike if you have them. Missile fleets will struggle due to close range and impracticality of syncing fire.
You will also want good engines (here you can trade range for a higher EP boost since you do not need to carry out extended campaigns with this fleet), to make sure you can either close with or evade the defenders depending on the tactical situation. It will also help to quickly regroup your fleet after the squadron jump to concentrate PD fire if the defenders use missiles. And finally of course you want to have as much tech into jump drives as possible, particularly the squadron jump techs to allow large jump squadrons (== more effective initial PD capabilities) and larger squadron jump distance (== out of enemy beam range until your targeting computers come back online).
However probably the most important thing is to outmass the enemy as much as possible. Against an NPR this is usually possible as they will only defend with one large fleet (plus maybe 1-2 small squadrons), against a human player race this can be tricky unless you have multiple borders. Thus in the latter case an important supplement to your jump assault fleet is a robust exploration fleet to find those alternate routes, either to surprise the enemy in his flanks or more likely to force him to divide his attention.