The CP2102 doesn't have the LED output pins that the N has. So designers have just put the LEDs on the TXD and RXD lines. Apparently it worked ok so long as you didn't try to go too fast. But the N will go much faster than the CP2102, so I think they had to put in the separate LED driver pins. I think you picked the right one.
I don't think I understand what you're asking about power sources. The problem with the VBUS pin is an example of what you have to think about when there are separate power supplies to different parts of the circuit. In your circuit, you have the V+ source provided by the USB cable when it's connected, and you have the +5V supply from your circuit that powers the CP2102N. The problem arises when you plug in the USB cable before you power up the N. If USB V+ was directly connected to the VBUS pin, and if the cable is plugged in before the N is powered up, then there would be 5V on the VBUS pin when VREGIN is at zero volts. That violates the Absolute Maximum ratings for voltage applied to any pin. The resistor divider is supposed to mitigate that.
So anytime you have separate supplies, you have to consider the order in which things will be powered up. If you powered the CP2102N from USB V+, then everything on the N side would power up at the same time, and you wouldn't need the VBUS resistors. But then you would have a problem at the other end with the CP2102N's pins TXD, RXD, DTR, and RTS connecting to the ATmega328 at 3.3V when the processor is still powered down. You would have to check the 328's data sheet to see if that causes a problem. I believe in that specific case that the 328 pins will tolerate that, but you would have to check. If my memory is right about that, you might want to look at powering the CP2102N from USB.
I should also say that one disadvantage of the way you have it set up now is that the CP2102N will be powered up when the 328 is powered up, and that may be wasting a lot of current if USB is only used occasionally.
One way to avoid all these problems is to have USB power up everything when it is being used, and switch off the 328's regular power supply.
One question - is your 328 a 5V part? The CP2102N TXD, etc., will all be at 3.3V. It might work anyway, but it would be better if they matched.