compiling as 64-bit doubles the size of longs
and pointers
Obese longs and pointers, imagine the horror - but, no, that's not the reason.The reason for why apps don't get compiled to 64-bits has more to do with the effort required to port said apps to 64-bits.
Truth is running 64-bits apps yields other advantages than access to more than 4GB of memory - a 64-bits app has access to the processor's 64-bits instruction set and some architectures allow access to more general purpose registers, memory-mapped files are easier to implement (MongoDB, last time I tried it, was unusable on 32-bits) and performance of applications such as encoders/decoders/encryption software is increased.
A 64-bits Flash would clearly benefit from the transition, even if you don't have more RAM.