When I first installed my front D60 I decided to stay with the stock 30-spline stubs to save money.......after a couple years I wish I would have spent the dollars to get 35-spline stuff. I've broken two 30-spline stubs and found a 3rd one twisted at the splines when I recently installed the 35-spline stuff. I was pretty lucky, but a broken stub can take out the spindle and cause other issues.
I also debated between going with the 30-spline chromo stuff (Yukon makes these) or 35-spline. As mentioned the 30-spline chromoly stubs are "supposed" to be about as strong as a Spicer 35-spline stub. I eventually decided to stop messing around and got 35-spline Yukon chromoly stubs and 35-spline flanges.
The problem with the Spicer 35-spline shafts seems to be that you can wallow out the yokes after a couple years of hard use, and then you start spitting out the c-clips and you get play in the shafts. 78Buford currently has this problem, and I know another guy who had to replace the 35-spline Spicers because of this problem.......never actually broke one, just wore it out. Supposedly this is not such a problem with the chromoly stuff because the yokes are better/harder material AND you use full-circle snap rings.
Regarding flanges, yes they are the strongest. I have heard of people breaking 35-spline locking hubs, though one of the guys mentioned above runs stock style Spicer locking hubs that were broached out to 35-spline and has never had a problem with them. I really don't think that Warn 35-spline hubs will break like a toothpick or anything, but flanges are stronger and I doubt you would ever break one.
It's also pretty easy to remove the flanges if so desired for street driving. Again, 78Buford has been doing this for quite awhile when he drove the truck to and from the trails.........takes maybe a couple of minutes to install/uninstall the flanges. The stock style pressed on cap covers work great for sealing up the end of the wheel hub and only require a couple taps with a hammer to install (cost around $12 for a pair of Spicers). Sure, not quite as handy as locking hubs........but if you NEED the strength of 35-spline stubs and flanges are you really in a situation where you need the convenience of locking hubs? Heck, even if you leave the drive flanges in place, and assuming everything in the front is in proper working order (ie. front driveshaft decently balanced, etc...) you will not hurt anything.