What does the Ultimate Pet Zapper do that the Pet Zapper doesn't? Which one should I use if I am looking to get a particular experiment pet?

I think that the major difference is that the Ultimate Pet Zapper has the chance to give out experiment pets. From what I've googled, the Ultimate pet zapper is more expensive, can zap your items(just lock them to prevent this), turn your pet minions into a slime(which can be valuable), and is half the time. I am not too sure however if some of these are not found in the first zapper.

the only way to get Experiment by zapping is to use the Ultimate one. It zaps them up randomly, so if you are after a particular Experiment instead of just any Experiment, it may take you awhile.

Also: v2 can increase or reduce stats, while v1 can only increase stats.