San Francisco housing is expensive BECAUSE of the incomes. Vancouver housing is expensive DESPITE the incomes. It's more of a housing issue than an income one. If incomes were higher, rents would only go up as well.
I don't see why we have to separate the two. It sounds like Vancouver faces both increasingly high rent and abnormally low salary for tech jobs (although I recognize that we might not expect Silicon Valley level pay).
Alternatively, SF/the US have extremely better salaries for tech jobs. I don't think this is a problem unique to Canada (but presumably its much worse because of easier access to visas).
I would argue the opposite, SF is expensive in spite of the incomes (consider across the board instead of just programmers).
I'm willing to bet if you were to map the relative rate of increase of income vs. property values over time that you would see that property values are increasing at a much higher rate than income.
I earn what could be considered a good salary, there's less than zero chance in hell that I could afford property in Marin today short of winning the lottery or massive liquidity event.