With the default prescaler of 128, the maximum sample rate is
9615 samples/s (16 MHz/128/13). It can be achieved by setting the ADC to
“free running mode”. Running analogRead() in a tight loop, the maximum
rate is 8929 S/s (16 MHz/128/14). As there is only one ADC, this is the
total rate for all inputs being sampled.
is there a way to disable muxing and select which one input is active
The MUX is a physical device that sits between the inputs and the ADC.
You cannot physically remove it. What do you mean by “disable”? You can,
of course, keep the channel selection constant.
I assumed that the muxer looks at each input in turn, but it may be
that if I only ever read from channel 0, then the mux will never
select another channel?
Indeed. You can think of the MUX as a 1P11T (one pole, eleven throw)
switch. Each time you change the MUX setting, it moves to a different
channel. If you don't change its setting, it doesn't move.

select which one input is active... isn't that what a mux does?