1K resistors - if there is no USB activity, the 1K's act like pullup resistor to 5V. The '328P can drive them high/low, external devices can drive them high low.
If there is USB activity, the 16U2 can drive them high low.
If there is both USB and external activity, then you have interfering signals.
Re: traces, via: I don't know. We only 1 Uno, it is secured onto a wheeled platform at the moment, I can't see the bottom to see if the vias connect to anything.
Re: the trace wiggle - also not important at the speeds being used, even at 230400 transfer speed the impedance would not be that critical.