First is it ok to have two vmdk of a virtual machine in two different datastores? are there any drawbacks to it?
Yes, there is no problem, just make sure that the datatstore have sufficient space and performance that your virtual machine needs.
If due to datastore size the second vmdk is in second datastore, if at a later time we want to perform a storage vmtoion, how this will be handled?
During the Storage vMotion wizard, clicking on Advanced option, you will have the chance to specify the place to each .vmdk, if the destination will be the same datastore or different datastore.
Note that if you're using Datastore DRS Cluster you may need configure the virtual machine to keep virtual disks separated.---
Senior Infrastructure Specialist