As far as I've tried, if you set a proxy in gnome-network-properties, making sure to use "Apply System-Wide" before leaving, synaptic *does* in fact use the proxy, through gksu, sudo or otherwise. The only caveat is that gnome-network-properties doesn't carry any proxy authentication values to the environment variables, but that is a different bug completely and can be worked around by using ntlmaps.
As far as I've tried, if you set a proxy in gnome-network- properties, making sure to use "Apply System-Wide" before leaving, synaptic *does* in fact use the proxy, through gksu, sudo or otherwise. The only caveat is that gnome-network- properties doesn't carry any proxy authentication values to the environment variables, but that is a different bug completely and can be worked around by using ntlmaps.