I think you're confused by the word stores. This doesn't mean that it moves 5% of your citizens that you already have to the colony, it means that you get an immediate 5% boost to your total citizen count that is stored in your colony. In other words, the citizens in the colony [u]add[/u] to your total citizen count and bolster your collections as if they were the result of any other population bonuses except that the number of citizens remains the same as your population grows or shrinks until you choose to repopulate it.
In the scenario I described you'd get 5,000 extra citizens paying taxes and thus a sizable boost to your daily collections for the price of repopulating your colony. If the nation that bought a colony with 100,000 citizens grew to 200,000 citizens without repopulating, they'd have 5,000 extra citizens in the colony, which only amounts to a 2.5% population boost. If they repopulated the colony it would give them a 5% population boost which would store 10,000 extra citizens. In the scenario you described, a nation that had only a handful of citizens on the home planet would still have 5,000 citizens (or 5% of their population the day they bought the colony or last repopulated it) stored for as long as the colony isn't repopulated or expired. That would be an even larger percentage of their total population relative to their ruined home country than the original 5%.
If this still doesn't make sense, there's more on Mars Colonies in [url=http://forums.cybernations.net/index.php?showtopic=64027&view=findpost&p=1711586]this post[/url].