Prior ot R2021b, you can set the scale of the y-axis in stackedplot using the undocumented NodeChildren property. However, the vertical reference line and text that tracks the mouse position will no longer work and a warning will continually appear when the listener is invoked. Therefore, that warning should be turned off (see below).
h = stackedplot(1:50,[exp(1:50)',exp(1:.5:25.5)']);
ax = findobj(h.NodeChildren, 'Type','Axes');
set(ax,'YScale','log')
% Turn off warning that
warning('off','MATLAB:callback:error')
% Don't forget to turn it back on
% warning('on','MATLAB:callback:error')
To set the yscale of a specific axis, n
% set(ax(n),...
