Did the Hetzer come out after they stopped Zimming vehicles or was it an exception to having Zimm applied.?

Hetzers came out after zimmerit was discontinued.

I thought Hetzers were put into surface in March 1944 and Zimmerit was discontinued in September.

Wehrmacht divisions got the first runs starting in July, 1944. Soon after they began using them to replace Marders as those vehicles suffered losses.

March 1944 was when they produced the prototypes for testing, so considering only about 4 or so months of trials and adjustments before field assignment things must have gone well. I think there were 2500-odd built by the end of May. I guess that since the contract was ordered a year prior they had plenty of time to engineer away a lot of stuff on paper. I'd hope after building so many different tank destroyers by that time that the Germans would have it down pat. Going from 0 to 2500 in two months is pretty awesome considering the circumstances of the war in Germany in mid-1944.

Now, as regards the other part of the OT which was zimmerit:

I've never seen photo evidence of it's use on the Jgpz 38(t), even though that stuff was discontinued in September which is, of course, after the start of vehicle production. It was certainly available to it for a few months at least. There were actually a number of vehicles produced that never received factory zimmerit, like the Wespe, the Pzkpfw II Ausf L "Luchs", and a few others - mostly smaller tank destroyers based on older designs and some anti-air. Proper tanks, the Stug's, and the newer tank destroyers like the Jagdpanzer IV's did get it.

Maybe the smaller vehicles don't get any because the armor is so crap that magnetic mines were considered the least of the crew's problems.

BMM (previously Praga) never joined the Zimmerit program. Their original tank destroyer, the Marder III, was an open-topped self-propelled gun, and didn't need protection from magnetic mines, as a simple grenade attack would destroy it. Then they switched over to the Jagdpanzer 38t, which, as a fully enclosed armored vehicle, technically ought to have received the coating. From a manufacturer's perspective though, Zimmerit was a pain in the backside to apply, requiring two days and lots of man-hours. I personally suspect that BMM's management simply never requested any, and the bureaucracy never noticed.

Zimmerit was always sort of a solution in search of a problem, as the biggest users of magnetic mines were the Germans themselves. The Soviets favored hollow charge hand grenades (similar to the German Wurfmine), or antitank rifles. Zimmerit was discontinued in September, 1944, when it was suspected of being a fire hazard. Tests subsequently revealed that it wasn't, but its use was never resumed, as nobody missed it. At war's end, the British captured over 100 tons of unused Zimmerit.

So, another question might be: After it was discontinued was it just left on vehicles and allowed to fall off with abuse? I can't see them maintaining it once it was no longer required. Would there be any cases where it might be stripped off?

Photographic evidence suggests that it was left in place. Stripping tended to be a post-war activity as part of 'restoration' efforts. Sometimes the museum then applied their own mixtures, in their own patterns (e.g. Saumur).