The ATmega168 has 6 or 8 analog channels but only one ADC. Each of the channels on chip is multiplexed already. The 168 (arduino) does not currently provide simultaneous analog to digital conversion. The external multiplexers add some overhead to the process.
According to the data sheet the 168 ADC has a maximum conversion clock speed of 200kHz and takes 13 cycles to make conversion. This means that a conversion takes about 65 uS (max of about 15,000 conversions per second). To sample all six channels will take approximately 6 * 65uS = 390 uS. Compared to the 65uS conversion time the overhead of the 74HC4051 multiplexers are negligable.
In terms of your original question, I have connected two arduinos to my computer for communications. It didn't seem to have a problem. Each arduinos maps to a different logical serial port.