Why when [A]/[HA] = 1, it is said that 50% of HA is deprotonated?

You may be thinking that [HA] means the original concentration but in this context it means the remaining concentration after deprotonation.
and
[A] represents the deprotonated
then
[A] / [HA] = 1 means that they are equal
and
protonated + deprotonated = the original 100%
but each are equal
so
each is 50%.

yes