You're asking a lot of questions, and it's always hard to guess at answers for posts like this because we don't know the specifics about the recruiter's message or their tactics. That said:
Does it matter if the candidate doesn't reply because he is not sure if it is a good idea to let the recruiter know about his situation?
Neither of the situations you described in your post are inherently "bad" in the long term sense. To put this another way: They are both valid reasons to decline right now, but still be a potential candidate in the future.
But the candidate wants to work for the company, and therefore may apply for a position in the company in the future. Will not replying a recruiter's reachout message on Linkedin affect his chance in the future?
If the candidate wants to work for the company, the question is really broader than this specific LinkedIn message. What is the candidate doing to develop relationships with people at this company? How does a response (or lack thereof) to this specific message fit in with the candidate's overall strategy? If a candidate is targeting a specific employer, a message like this may be a golden opportunity to establish a relationship - even a minor one - with an important decision maker (a recruiter) at the target employer. I had a mentor once who taught me to "never waste a crisis." When you see something that you're worried may be perceived as bad, instead of focusing on that bad, look for a way to turn it into something good - developing a relationship with the recruiter, in this case.
What would you do if you were the candidate?
Gonna skip this one, since "what would you do" questions are not usually helpful in the context of this forum. You need to figure out what YOU would do, not what WE would do.
Is it normal that a recruiter in a good company sends out messages to tons of candidates, and doesn't track who has been contacted, and doesn't care if there is reply or not?
Yes, many recruiters at large corporations have pro LinkedIn accounts that let them spam potential candidates. They may not even know or care who the specific individuals are, and they certainly won't think badly of you if you don't respond. They're likely not keeping a scorecard on who didn't reply. That said, we don't know if that's the case here, and personally, I don't think it matters since as I mentioned above, I see this situation as an opportunity, not a problem.
I will preface my answer to your question with some questions:
What is your strategy for engagement with this potential employer? Do you know how they recruit? Do you know how they find, filter, and evaluate candidates? Where do they post jobs? Do they participate in career fairs or other recruiting events?
So, finally, Yes: you should respond to this message with a brief mention of why you're not going to pursue the current opportunity, but you also need to consider making this message a part of a larger strategy:
Hello So-and-so, I appreciate your message but I will have to pass up the current opportunity because of X. However, I have been following your company on X and am interested in X type(s) of roles in the future because of X. I know your company will be represented next semester on campus, perhaps I could arrange to speak with someone then? or: I know you often post jobs on LinkedIn, I will be looking out for X role in the future.
And, if this recruiter isn't already a LinkedIn connection, I'd go ahead and request.