There's quite a few unknowns here - just how many LEDs, resistors, configuration (from description it sounds like they're all in parallel*) and physical layout+housing all affect things like the heat dissipated.

But just to answer your questions...

Yes, you should be concerned if the resistors are getting hot and it's just meant to be a nightlight. Nightlights should never run hot :)

Yes, two equivalent resistors in parallel should as a set have half the resistance and double the max power dissipation. At 50 Ohm (from 2x100 Ohm in parallel) you do get a bit less current and thus a bit less power dissipation required, but not significant.

I guess the missing question is "Why doesn't this seem to be the case?". I can think of a few reasons when measuring, but nothing on the order of the difference between 'uncomfortably hot' and 'no noticeable heat'.
You may wish to double-check the resistors.. maybe they're not the value you think they are (is the 47 Ohm resistor a 4.7 Ohm resistor?), or they're not the wattage rating you think they are. Or maybe I, and two people I asked because as far as I know this shouldn't be happening, am missing something.

As a more general note, you could also try to wire more of the LEDs in series. This may not be an option for the auto-cycling RGB LEDs (you'll have to try and see if they're okay with being in series - if they're not, failure modes are usually being stuck at the initial color, or an erratic color program) but for e.g. these LEDs, even at their upper voltage drop range of 2.3V, you can have 2 in series, and at their lower voltage drop range they'd still drop 4.2V, leaving only 0.8V to get rid of across a resistor and thus less heat dissipated. Of course there are down sides - if 1 LED fails, the other does nothing / dies pretty quickly.