As of May 2016, there are 11 currencies available, more may have been added later, but I don't know.
Do note, though, that you only get to choose between the currencies that are relevant to your country, plus USD. Here in Sweden, I only get to choose between USD (available everywhere), EUR (because Europe), and SEK (local currency). Someone in Canada would have USD and CAD, and someone in USA (or any place where the local currency is not supported) would only have USD, which I guess is your situation.
The price you see is the price you pay. If you're in Malaysia, you see GOG's prices for Malaysia, the fact that you only see USD makes no actual difference on the price (but I'd wager that it's the same as the US price), if you want to know how much that is in MYR, go to a currency conversion site and look it up.
Also, you would pay the same value regardless of which currency you'd use, so a game that cost 9.99 USD
in USA would probably be 9.99 EUR
in Sweden, about 10.64 USD if I switch to that currency, or 94.78 SEK if I chose that.