For a headless server with virtual desktop, try using vncserver-virtuald.service instead:
sudo systemctl enable vncserver-virtuald.service
sudo systemctl start vncserver-virtuald.service
Or use vncserver-x11-serviced.service and add hdmi_force_hotplug=1 to /boot/config.txt as @bigmac described to view the same desktop as presented over the HDMI output.
If you download the python-numpy_1.16.2-1_armhf.deb file (and all the dependencies) and transfer to the Pi they can be installed with:-
dpkg -i python-numpy_1.16.2-1_armhf.deb
apt is actually a front end for dpkg which automatically manages dependencies.
Depends: python (<< 2.8), python (>= 2.7~), python2.7:any, python:any (<< 2.8), python:...
Making a few assumptions about how everything has been configured, you can essentially just directly extract the contents of a *.deb into the root of the file system. You should never, ever, do this on a system where apt is working properly, but if apt isn't available, here's what you do.
BUT FIRST, A WARNING!
MANUALLY INSTALLING PACKAGES AS DESCRIBED ...