IME one can get 'astigmatism' type effects such as only being able to get 'one side' of your FOV in focus at a time [also w/ an f5 scope coma (which you can't do anything about short of getting a paracorr) will start to come into effect- mostly away from the center of the field though].

IMO, 'masking', 'stopping down' or some form of reducing your aperture is mighty silly [unless just to remove a mirrors turned-down edge from the image (or in the event your mirror is of spherical figure rather than parabolic)]. If you want a smaller aperture or longer f-ratio scope- why not just get one [with a newt, 'stopping down' is NOT the same... the relative increase in obstruction % can become dramatically detrimental].

Jupiter being lower on the horizon IS, under the majority of conditions, going to make the 'seeing' of it worse [and probably nearly 'exponentially'- the amount of atmosphere one is looking through doesn't increase linearly as you drop in declination].