5.0.1 probably added the beeps as one of Apple's "features" to remind you to take the watch off the charger, so they don't over-charge, instead of admitting there may be a charging problem.
That's not a good way to run a successful business, so I doubt that's the intent.
Anecdotal datapoint: overnight-charged my Nike edition S4 for the first time last night, using my old plastic charging puck I got with my OG Sport Watch that I've used well over a thousand times by now. Put the watch on, it dinged, then - maybe because I set it to auto update to 5.01 overnight it dinged a second time some short time later. I hadn't fallen asleep, but was well on my way. A bit annoying!
Only happened that one time though.
In the morning it was completely cool when I took it off the puck, and hadn't dinged any more either. My OG would sometimes be warm, sometimes cool, sometimes partially inbetween. It varied. I assume the same pattern will hold now as well.
Also let my S4 sip a bit of juice yesterday from my macbook, but that was only a small partial charge, using an original Apple charging cable I bought for travel purposes for my OG Sports watch over three years ago. Only made the standard ding when I put it on and then nothing more, although it charged for only like 10 minutes maybe and never reached close to full power.