Should i cut it in half where the trunk separates in two so it has only one main trunk ?

leave it alone Meyers are bushes and will probably send out more low level limbs.

In fact, I am mostly worried about the v-shaped crotch. I wouldn't want this to split in two later on under the weight of the fruit... What do you think about that?

The crotch angle of your tree is ideal for healthy stress free long life. When the tree gets older you can alway run a wire between the 2 branches but the need is very unlikely.

Is it because it is a rooted cutting that the leaves appear to be much larger than the ones i see from pictures of other meyer lemon trees?

Young trees tend to have larger leaves from what I've seen. Also when citrus grow indoors with less then perfect light conditions they will also grow larger leaves to help capture as much light as possible. When you bring your tree outside in the spring, It will probably grow new smaller summer leaves.