How do manufacturers/kit providers determine Vne? Vne defines the maximum indicated airspeed which should not be exceeded. And clearly, doing so would result in "bad things" happening like flutter, etc. Presumably manufacturers do some sort of design work to determine likely Vne but how do they test for that? Exceeding Vne would put the aircraft into a structural failure situation would it not?
$V_{ne}$ is typically set to about 90% of $V_D$, the maximum design dive speed.  This difference provides a safety margin.  Above $V_D$, damage may occur due to flutter or structural failure, or controllability considerations may make the aircraft unflyable.  The aircraft is not guaranteed to fall apart at $V_D$ due to additional structural and manufacturing margins.  

During flight test, the aircraft is flown above $V_{ne}$, up to, or close to, $V_D$.  Appropriate safety precautions are taken, e.g. parachute.  Any failure below $V_D$ indicates a design or manufacturing issue that must be resolved prior to certification.

The limitation to flight below $V_{ne}$ (as opposed to $V_D$) during regular operations provides protection against airspeed measurement errors, pilot errors and some margin against structural degradation over the lifetime of the aircraft.