Lots to unpack there tracy so I'll try

"As the covid-19 vaccinations are governments sanctioned, will they bear the cost of medical expenses of the individuals that suffer from myocarditis, allergic reactions, shingles and bells palsy?"

I'm not sure if you mean "mandated" or "sanctioned" but ACC will cover, in the normal manner, injuries that are not a usual consequence of having a vaccine. Eg if a person has a red mark injury around the puncture site this would not get ACC cover as it is a usual consequence. By if there was an injury coming from a reaction to the jab then it would be.

"There is a portal for reporting, but what of the investigation process and potential outcomes?"
If you have required the employee to get a jab and there has been a subsequent injury I would expect your usual incident reporting and investigation processes to kick in. I'd also note an employee can't "sue" an employer where ACC provides cover. But the employer can't rely on that if ACC doesn't provide cover.

"Will ACC cover any costs if there are long term health effects, hospitalization or payout to family members in the event of a death?"
Most likely yes - if the injury is not a normal consequence of the vaccine.

"What about the people, who have had a bad reaction to the second covid-19 vaccination and do not want the third, or any booster shots that follows? What are workplaces to do then?"
I hope you are asking why you are requiring vaccination in the first place. But if you have decided to go down that track then your test will more likely be a requirement for a person to be "fully vaccinated" rather than just receiving a certain number of jabs. If a person isn't / can't be fully vaccinated then you apply your protocol as if they were not vaccinated in the first place. That is, presumably the person may lose their job.

"What medical monitoring is proposed for staff that do not want to get the vaccinations, for the workplaces who do not want to let their staff go, due to current staff shortage issue? Where are the guidelines available around this topic?"
First issue is why do you want to medically monitor? And who are you going to medically monitor. Don't assume it is only the un-jabbed who can bring covid into your workplace. Very tricky question - no easy answer because you are going to have to look at health monitoring protocols, managing health information etc etc. With RAT (Rapid AntogenTests) it may be simpler to set up a protocol that requires a suspect person to bring in a negative test result from a pharmacy or other such RAT provider. Anyone with covid type symptoms shouldnt be at work.