2 corrections/updates:
Yes, You will be charged for the Storage Capacity you are using for storing your VHD files in Blobs.
[Update] Since VHDs are stored as page blobs, you will only be charged for the data you're storing. Let's say you created a 30 GB VHD but storing only 1 GB of data in it, you will only be charged for 1 GB. All empty pages are not charged.
Regarding the transactions,If your VM and the Storage accounts are present in the same datacentre you will not chaged.
[Correction] This is incorrect. You're always charged for storage transactions. You're not charged for data egress if both your VM and storage accounts are in the same data center.