What you could use is the -geometry option for nautilus shortcut.
For instance, I could set Super+E (which is same as Windows shortcut for opening "My Computer" ) to nautilus --geometry 250x250+0+0 . The geometry option is defined in man X page as WIDTH+HEIGHT+XOFFSET+YOFFSET. +/- can be used and man page defines the corners as:
+0+0 upper left hand corner.
-0+0 upper right hand corner.
-0-0 lower right hand corner.
+0-0 lower left hand corner.
With terminal , that's a little different because gnome-terminal treats geometry option as in rows by columns. So gnome-terminal--geometry="250x250+0+0"` will open a window that is just horribly large.
What you also could do is to alter the .desktop files in /usr/share/applications folder, particularly the Exec= line to have the geometry option, so that launcher icons also can spawn windows with specific size