1- Do we have to answer the question no. 18? Which is related to, humanitarian and Compassionate Grounds. Her total is less than 730 days and she has been a Permanent Resident for less than five years ago. In our case we don't need to answer so can we leave that one empty? Or what?
You don't have to worry. If she is a PR for less than 3 years, it is not physically possible to not meet the residency requirements because she is allowed to stay outside Canada for up to 3 years in any 5 year period. She can not be denied a travel document if she can still has time to stay in Canada for 730 days in her first 5 years.
2- My family stayed only 16 days in Canada so legally my son can get the Travel Document right?
Yes, see 1.
3- For TD, Do they need to show/submit original document, other than previously visa stamped passports? Like landing papers? Sin Card? PR of wife as my son was accompanying with my wife, do she also need to show her PR in Canadian Embassy?
I am not sure what they have to show. You should ask the embassy. They will definitely not need a SIN card. Either the passport is enough or maybe they need the landing papers too.
4- Can we send PR through courier? Or any other way to send the PR of my wife to her.
Yes, you can send it through courier.
5- If someone is coming back to Canada on TD, then do they ask some strict questions on airport? Will they ask why you left Canada without having a PR? Or something likes that?
I know of one person who did not apply for a travel document as he was visa exempt so it was enough for him to have his landing papers to get in. He felt that the immigration officers were unpleasant to him and wanted to know why he had left Canada so soon after landing. So.. it is possible that she will be asked that. They can not deny her entry to Canada. All she has to say is that she had to go back to attend her sisters wedding. It is not under her control to postpone her sisters wedding until she gets her PR card and she did not want to miss it. That is a reasonable explanation.