the better question may be: how does one defeat RA in full swing?
Well, for defeating Ra, one must first idenitify the RA weakness. The RA requires lots of fleet logistics to be really useful which translate into high maintenance costs, and as stated, phase jumps.
RA allows you to completely ignore all maintenance costs entirely, because you no longer need to make money via taxes or trade. RA itself finances your entire empire and salvage is not affected by your maintenance level.
So deafeating RA in full swing will surely requires targeting specifically the phase jumps and the various ressources extractors to cripple its economy: you can't win a direct confrontation with someone that have unlimited supply for ships. So you need to play a cat and mouse game, especially since all its planets are only phase jump away from the other for him.
Phase Gates are not that vulnerable. There's no need to put them out on planets out in the middle of nowhere. Yeah, killing them will reduce the power of RA, just like killing trade ports will reduce trade income. If the player has the power to kill the gates then he probably has the power to take the entire planet so it's moot.
You yourself note why it's extremely difficult to harass a Vasari in this manner - all his planets are connected by a single phase lane effectively. Your harrassing fleet may have to make several jumps, only to find his entire defense fleet waiting for it at every turn. This is magnified by Vasari's superior phase jump tracking.
Targetting resource/economy structures against a player with RA is all but worthless. The vast bulk of their income comes from RA itself once it's in full swing.
And it should be also noted that there is no control on the kind of ship that will come from the gates. You can perharps use this to make him to have a mis balanced fleet: don't target flak and carriers, and it will surely ends up with a fleet with only those. And YOU can adapt your fleet composition
There is a control on the type of ship you get. It's Salvage. Salvage the ship types you don't want, gather up the ones you do. Takes a bit of micromanagement, but done properly a Vasari player with 3-4 planets can produce more ships than an empire with 20+ and have so much money produced from salvage on the side they won't be able to research fast enough to spend it.
Last time I managed to get around 9 gates up, I hit max fleet supply faster than I could research each next level, and had tens of thousands of credits, minerals and crystal left over. What am I gonna spend it on? You don't have to pay for any ships, you get heavy cruisers and LRMS and anything but support cruisers, colony ships and caps free of charge. You don't need to research ship prototypes. You don't need to capture planets except to deny them to the enemy, since 3 planets give more than enough gates to steamroll the galaxy and 5 becomes ludicrous overkill where you can lose every ship you own and replace the entire fleet in a few minutes. Really, the only thing you need once you have RA up and running is to salvage the unwanted ship types and use that to queue up weapon/damage upgrades, and try to time producing capital ships/support cruisers in the short window where you have that supply free before it fills back up again.
Rushing RA is not always a good idea depending on map, but it's still the juggernaught of sins once it does come out. And if you can rush it (team, and FFA scenarios)... well, I got a fully maxed fleet supply of heavy cruisers, flaks and LRMS in about 50 minutes. I haven't been able to come anywhere NEAR close to that actually researching heavy cruisers and trying to produce them. The maintenance cost gets too crippling to try and max it out that fast for anything but RA-strategies, let alone actually paying for the research to get heavy cruisers AND an economy.