Usually, when it comes to fixing a computer, it's a hassle to narrow down the exact problem. So sometimes computer shops just try to troubleshoot a specific area i.e. motherboard and conclude that it's easier to just replace the entire thing rather than fixing the actual issue. Sure it's costlier, but that is for the customer to worry. And you can't really blame them. If the problem only requires a simple replacement part which cost RM5, then there is no guarantee if the repair won't cause other issues, apart from the minuscule profit made from the repair versus the time consumed (small components are much harder to replace than an entire motherboard).

As for the price quoted, it could be the shop is thinking to get a refurbished motherboard and replace it to yours.