How many logical fallacies are present here?

I think there are 2 fallacies.

Person 2 can't believe that a company wouldn't possibly decide something just for profit while completely disregarding any harm to third parties, therefore it doesn't happen. This is argument from incredulity .

Person 1 can't think of a good reason for decision Y, therefore no such reason exist. That's argument from ignorance. ("absence of evidence is not evidence of absence"). And to address the aforementioned seal example, if clubbing seals involves exterminating select seals members that are harmful for the rest of the seals, for example sick animals that need to be isolated or killed if can't be treated to protect the rest, then that's a beneficial outcome for the seals in general. Actually, I think I had heard in the past that there was an operation conducted officially by the country's state and that was proposed by environmentalists (I don't remember the country, Australia maybe?) because the overpopulation of some species was endangering the environment due to the rapid depletion of resources caused by the overpopulation. If they didn't act like that then a bunch of species would be affected or endangered, including the overpopulated species itself - I think that can happen especially for introduced species. 
So, it is possible sometimes that there are reasons that we can't imagine but they absolutely exist, even if neither our interlocutor nor we can express.

>Multi-billion dollar corporation X makes decision Y.

      Question is: “So What?”

> Person 1 offers criticism against decision Y, finding it has no possible merit and only causes problems.

     Question : Why is Person 1 concerned unless he is affected directly or indirectly?

     Question: Why does decision Y have “no possible merit ?”

     Question: Why does decision Y “only causes problems?” 

>Person 2 argues that "there must be at least some good reason why decision Y was made".

     This is speculation and premature.

> Person 1 asks for reasons, and person 2 states he can only make guesses. These guesses are based off of poor speculation and as such are easily proven wrong.

     Person 1 is not the participant who should be asking for reasons because Person 1 is the person propounding the proposition. He bears the burden of proof of his initial proposition before the discussion may proceed. 

>Person 2 holds on to the belief that decision X must have been done for a good reason, and that person 1 is not an expert and is just being ignorant. The claim that decision Y has no merit is dismissed, saying "you can't really know that for sure" (despite any strong claims or evidence presented).

      So what? Person 2 is being sucked into an illogical discussion. 

I find this example to be kind of confusing. Partly because of the vagueness of the example overall, but I'm also finding it hard to pin down what you'd consider to be a good reason.

In your followup comment, you mention that Person 1 is primarily viewing this through the lens of how the decision affects Group Z. Did the decision maker in this case say or imply that it was supposed to be to their benefit? Person 2 then says the corporation could save money, in which case the corporation would be focusing on its own interests. Realistically, corporations acting in their own interests tend to be pretty ambivalent as to whether their decisions are a net positive or a net negative for others.

But then there's "The corporation believed it would be a good idea." I can't really square that with the rest of it, as it's hard to envision a scenario where a decision maker believes they're making a good decision, but has no reason for believing that. Did they just make an arbitary decision and not think about it because it sounded good? Was the decision based on some nonsensical objective? Was the intention behind the rule good, but the implementation just was poorly thought out?