It doesn't directly affect the baljoints, however lowering the subframe on the side you are working on will make the job drastically easier. the balljoints of a 96-07 taurus is pressed into the buttom of the spindle, where it is then connected to the lower control arm. Under normal circumstances there is nearly no clearance for the spindle, once removed from the strut and lower control arm in order to have the old ball joint pressed out and new one pressed in , to be assembled back with the lower control arm(since you will have to mount it back onto your struts first, as there woulden't be enough cleanence to put the strut back into the spindle, if you decide to make the spindle-lower control arm connection first) , but since the lower control arm itself is mounted to the subframe, lowering the subframe slightly will also lower the lower control arm so when you press down on it to gain clearance it can go a lot lower compared to if the sub frame isn't lowered, give you a lot more room to work with when trying to force the ball joint shaft into aligning with the pivot hole on the lower control arm. It is possible to re-attach the spindle-lower control arm without lowering the subframe(we did the driver side this way) but it is almost certainly take a lot longer then to simply lower the subframe slightly , reassemble the spindle onto the strut first, then with someone else applying downward force to the lower control arm, push the strut-spindle assembly towards it, re-align the ball joint shaft on the buttom of the spindle with the hole on lower control arm, and release tension from the lower control arm in order to re-attach them. rest of reassembly work is a piece of cake.