it's because of the T which runs into the "un". cet is the correct pronunciation in this case. Also as far as the grammar is concerned "cet" is an adjective so you would need to say something like "cet enfant est japonais" you couldn't put "cet" before "un". This means that whatever the sound you would need to write c'est for it to make sense.
But they aren't synonyms. "Guy" is both more casual and more general than "boy". A guy could be any person, usually but not exclusively male, of any age. A boy is a very young male person. There are probably occasions when you could translate "garçon" with "guy", but without context it would never be my first choice.
Just a note for the non-anglophones among us: using guys (plural) as TempleRachel does above, to address or refer to a group of people of any gender, is very, very casual, but common enough, at least among younger people. (Note: it was common among younger people when I was one, too. Our English teachers used to mock us girls for using it)
However, at least in my part of the English speaking world (Western North America), a guy (singular) is only ever male.
TempleRachel That's not quite right. "Hey, you guys" is the use of the generic masculine. For example, in the days before political correctness, people commonly used Man and Mankind in the generic sense. When you say "you guys" to a mixed group, you have defaulted to the masculine plural to include everyone.
Following the link from pietvo above, I discovered that 'C'est' is used here because it is followed by a modified noun (the noun has an article and may, as in this case, have an adjective). I would tend to translate it into English as 'This is a Japanese boy, rather than use 'He', but it's because I think it sounds more natural to me, without any extra context to pin it down. As part of a conversation, I think that either 'he' or 'this' could be used, depending on the nuance you want to convey, but in French it would remain "C'est un garçon japonais".
No. "Il est un garçon japonais" is wrong. You "must" use "c'est" before a noun that is modified with any determiner (un, une, le, la, du, etc.) http://www.frenchtoday.com/blog/cest-versus-il-elle-est
Most adjectives go after the noun. However, there are certain words that go before the noun.
Many people swear by the BANGS (beauty, age , number, goodness, and size) mnemotic to remember which ones. Unfortunately, it is more if a guideline because there are adjectives that would relate to, say, size that would not go in front if the verb.
I would recommend googling "french adjectives before noun".
Also keep in mind that some adjectives change their meaning depending on whether they go before or after the noun.
there is an exercise on duolingo that does not accept "C'est un homme japonais" as a translation for "He is a japanese man.", but instead requires "C'est un japonais." in the comments section the reason given as an explanation is that "C'est un japonais." clearly shows that subject must be a man because of the gender. Yet this sentence, "C'est un garçon japonais." is an example of why further clarification might be needed. One could even be referring to an inanimate object, like a film or book. Anyway, in a stand-alone sentence with no other context, it makes sense to specify who/what is japanese.