One suggestion I can make, which DCStrom also mentioned is to zip-tie your spokes together where they cross. This will prevent any additional damage to the rim, swingarm, etc. We did this on our desert racing bikes but for a different reason....if we broke a spoke we did not want the spoke to jam itself into the chain, brake rotor, etc which could cause you to go from racing speed to a crash in a heartbeat!
The nipple issue
is due to Yamaha's design, which I think is great, but does have it's drawbacks. On the plus side it is real easy to replace a broken spoke; since there are no nipples in the rim, you don't have to worry about sealing each spoke hole in the rim; it's easy to true the wheel and adjust spoke tension (try that with the spoke system BMW uses on the GS's). On the negative side, due to the nipples not being retained by the rim band/tube (like on regular spoked wheels), if a spoke loosens up then there is nothing to retain the nipple and it will eventually come off. And you end up with a flopping spoke. Hence the suggestion to zip-tie the spokes together. All bikes with spokes should have their spokes zip-tied.
You can use locktite on the nipple, but you will not be able to use a torque wrench to check the torque on the nipple, but then I have never used a torque wrench on spokes, in my 40+ years of riding/wrenching. Neither have any of my fellow riders and racers. We always use the 'ping' method to check for loose spokes and check for the wheel being true by spinning it on the axle using a simple pointer to check for runout and adjust as required. We did/do this usually after any big hits or every couple of rides.
I agree with MarkJenn that this really is a maintenance issue (somewhat exacerbated) due to what I believe is flexing of the cast aluminum hub, specifically the nipple bosses that might be a tad undersized. But spoke wheels are not maintenance free, that is one of the reasons that cast wheels became so very popular. I am sure that a large number of ST riders have not had spoke wheels before, so there is widespread unfamiliarity. Especially with a almost 100hp bike!
I have only had a couple of loose spokes, they required no more than a quarter-turn to take care of. These were within the first few thousand of miles. Nothing since.
Just keep a eye on them and I am sure after they 'seat' then the maintenance will be become infrequent.