From NOAD:
represent (v.) (be represented) (of a group or type of person or thing) be present or found in something, esp. to a particular degree : abstraction is well represented in this exhibition.
When the author talks about low representation, that's the sense of the word being used. In other words, Atlantic cites are not well represented on the list. There is a list of cities, and relatively few of these cities are Atlantic coastal towns, and none of those cities rank very high on the list.
Why is this unsurprising? That tidbit alludes to a perceived bias that Atlantic Canadians are already well aware of: the rest of the country doesn't seem to think we live in the nicer parts of Canada, at least from a livability standpoint.
Therefore:
- You won't find many Atlantic cities on the list best Canadian cities in live in, and
- This only confirms what people in those Atlantic cities already know.
As for whether or not these cities truly deserve to be left off the list (or be near the bottom), that's another matter, and there's not enough context in the snippet you've provided to say. However, I went to the source that you linked to, where I found:
when you consider their methodology, it should come as no surprise that half of the top ten are in the west, primarily in Alberta. There is a heavy weight on wealth and demographics. They also indicate that intangibles such as scenery and attractions are not considered, as “This isn’t the best places to visit, it’s the best places to live.” Weather, therefore, is part of their consideration.
The writer is hinting that you need to take this list with a grain of salt. Whoever compiled it puts little value on beautiful ocean views, and dished out heavy penalties for potential stormy weather. If a different panel used different criteria, where beautiful ocean views were weighted more favorably, and weather wasn't so much of a factor, their list might look very different, and Atlantic cities would be better represented. However, it seems like residents of those Atlantic cities are used to people overlooking their strengths and benefits, and focusing on the drawbacks, which is why they won't be surprised to find very few cities in their region on the list.

The beach at Middle Cove, a mere 10 minutes from the Atlantic city of St. John's
There's an old adage about certain places:
It's a nice place to visit, but I wouldn't want to live there.
The writer is saying that, by ranking Atlantic cities so low on their list, that's pretty much how the writers at MoneySense probably feel about many eastern Canadian coastal towns.