To find the tag of axes1, you can just get it directly:
Tag = get(handles.axes1,'Tag')
However I would expect that the code you had (set the current axes to handles.axes1 and then get the current axes tag) would also work.
Are you sure that this axes actually has a tag set? If no tag has been set, it will return an empty string.
UPDATE BASED ON COMMENT:
Aha! The scatter() function (like most of the high-level plotting functions), when called on an axis that is not held, will internally clear the axis (deleting it and its Tag) before plotting to a freshly made axes.
figure, plot(3,4), set(gca,'Tag','qqqqq')
get(gca,'Tag')
scatter(4,3)
get(gca,'Tag')
Instead, you can call hold the axes before you call scatter, which will keep your old axes including its axes tag:
figure, plot(3,4), set(gca,'Tag','qqqqq')
get(gca,'Tag')
hold on
scatter(4,3)
get(gca,'Tag')
If you still need to work from a clean slate (ie, you want to clear the axis, but keep its Tag), then you can selectively delete all children of that axis:
delete(get(gca,'Children'))
scatter(...)
