In practice it helps quite a lot, as it enables sampling the current far away from the switching cycles even at high speed. This can be noted on HW4 where a commanded constant current will give a non-linear acceleration: it will be linear to around 60% of full speed, then it will decrease for a bit up to around 80 % and then it will increase from 80% to 100%. If you give full throttle and pay attention to this, the effect is very obvious. I spent a lot of time trying to work around this, but it is not easy as it depends on many things and behaves differently on different motors and voltages. The current simply becomes noisy and gets aliasing at certain motor phase angles at high speed when using two shunts. Analog filtering is also not possible in the same way as with three shunts as the rise time has to be very fast at high modulation for two shunts to work. The VESC6 has a smooth linear acceleration from 0 to full speed, and this is mostly because it uses three shunts.
Two phase shunts are slightly better than two low side shunts, but three shunts are still the best. I would prefer three low side shunts over two phase shunts in general, if that is a choise to be taken in a design (e.g. when making hardware that supports 100+ volts).