Malaysia was added so that the UK AI wouldn't have to deal with defending it with troops since they are already spread out as it is. I believe you can easily annex them, but you also fail to recognize that the UK can buy ludicrous amounts of rubber per factory from them and that 80% of their civs go to the UK.
Same goes for Dutch East Indies, they're still pretty useless so long as you send in something better than rabble to conquer them.
I think the point was that the UK no longer earns CIVs from sales of Malayan rubber, which hurts the AI's ability to build up its economy. Human players can work round this using the methods you describe.
Hopefully one day we'll have a Southeast Asia DLC with a Malayan ("Malaysian" is just a misspelling in the 1940s) Focus tree that corrects such issues by modelling the great British-owned plantation firms and perhaps the International Rubber Council, which was as important in 1930s economics as something like NAFTA or TPP today.