RC batteries mostly get hot because people are impatient, and are unwilling to use lower-rate chargers.
Charging cells in series is a real problem. How severe it is depends on how closely the cells are matched: if they're not very close, some will wind up either under- or over-charged. Over time, the problem can get worse, as the mismatched cells get more damaged by heat during fast charging (the "stronger" cells have to dissipate the extra energy as heat while the weak ones are getting topped off) or heavy load (the weaker cells have to work harder). Both the packs that came with my Ryobi tool kit have this problem: after a couple of years of moderate home use, the charger started refusing to even try to charge them, because one or more cells are shot. And the cost of getting them repaired (which has to be done by a third party, because Ryobi won't do it) is higher than replacing them >
Separate charging of the individual cells is definitely much better, but the vast majority of people, especially in "First World" countries, strongly prefer the convenience of battery packs that are easy to swap quickly, even though the life-cycle costs are somewhat higher.
There's quite a bit of literature about this available on the web, if you want to learn the intimate details.