How will knowing the resonance frequency help you? The usual way to make a fence charger is to apply rated current to the primary of the coil for a few milliseconds, once a second. The fence chargers I've seen in the past used a mechanical gizmo to pulse the spark coil once a second. You don't need to know the resonance frequency; it all takes care of itself.
But, just for grins, I measured the resonance frequency of 3 automotive spark coils I have lying around. I connected a 200 megohm resistor to the secondary, in series with a 2k resistor, then to the minus terminal of the coil. I passed about 1 amp through the coil primary (with a .22 uF cap across the primary) and then interrupted the primary current with a mechanical switch. I monitored the voltage across the 2k resistor (which was about 1/100000th of the secondary voltage) with a scope.
When the primary current was interrupted, there was a voltage with a decaying sine wave characteristic at the secondary. The peak voltage was about 10,000 volts, and the frequency of the ring (the coil resonance) was about 2.85 kHz for one of the coils. The other two coils also had a resonance frequency of around 3 kHz.
I measured the resonance frequency without the .22uF cap across the primary. The resonance frequency increased to about 3.1 kHz. The primary cap has very little effect on the coil resonance; it's almost completely dominated by the self resonance of the secondary. But, the .22uF primary cap is needed for proper operation. It absorbs most of the spike that would otherwise appear at the primary due to the leakage inductance.
You should also know that automotive spark coils aren't designed to withstand the voltage that appears at the secondary when they are operated with rated current, and with the secondary open-circuited for extended periods of time. When they are connected to a spark plug, the breakdown of the plug gap limits the secondary voltage. You'll say, everybody who has ever worked on a car has disconnected a plug to see if there's a spark, so you might think that the coil won't be hurt by doing that. But running open-circuited for extended periods of time can be harmful to the coil.
If you're going to use an automotive spark coil to charge a fence, there will not be a spark most of the time; you'll be running open-circuited. Maybe if a cow or some other conductive object is touching the fence, the voltage would be limited; but most of the time it will be open-circuited. So, you should run the coil at a reduced primary current, or I suppose you could connect a spark plug across the secondary to act as a voltage limiter. With a spark plug in place, you will still get a fairly high voltage out, and you'll protect the coil from internal arc over.