Your SVG documents contain unused and/or invisible geometric elements. Since these elements are in there, they are taken into account when calculating the size of the displayed graphic. If you remove these unnecessary elements, yEd does no longer reserve more space than expected.
E.g. I have removed (or rather commented out) two unnecessary <path> elements from your network-server-vm and now it displays fine. (Using a diff tool, you will spot my modifications right away.) The same approach yields a nice version of your generic-1u-server, too.
A good approach for finding problematic elements is opening the SVG document in Inkscape, zooming far out, and then stepping through the elements in Inkscape's XML editor ("Edit" -> "XML Editor"). Each time an element is selected in the XML editor, it is highlighted in the main drawing canvas (if not, it probably lies outside the currently displayed area and you need to zoom out some more). This way you can easily determine if the element actually contributes to the graphic or not. In the latter case, it should be removed (which can be conveniently done in the XML editor).