Focus Mk3 TDCI. 

Another aircon question, must be the time of year? LOL

When I use the aircon, there is a (loud enough) hissing sound which sounds like its behind the dash, its intermittent, but always there when the compressor is turned on.

I had the aircon refilled 2 years ago after having the aircon radiator (condenser?) changed, I'm not sure if it was holed or not, but visually it looked battered. The guys did have "issues" filling the system up, but I didn't really have the upmost confidence in them anyway, but it was nice and cold after. I hear the machine tests they run on vacuum can actually give false readings and seal leaks while the vacuum is running?

It may be my own fault as I hardly use the aircon. 

Before I pay and have the system leak tested and then refilled, just to have it not work again in a year or two, anything ideas on the noise?

The Vac test can definitely pull seals in which then then leak under pressure.  They should run a pressure test as well by filling the system with Nitrogen after any repairs though.

After 2 years it's likely to have lost some gas and need a top up or refill, the Mk3s aren't good at holding gas and the noise is often caused by low gas.  Might be worth leaving it running for a few trips to see if it clears before spending on a regas.