There is no special pricing for the HPC Scheduler, other than the components it uses:

CPU hours - head node role, compute role, and frontend role. You will be billed for the number of cpu hours those machine use, which depends on the type of machines and the number of instances you defined (the default is 5xSmall node) during the deployment.

Storage - to hold your deployed HPC applications, so you will be billed for the storage (GB/month), and for storage transaction (that can reach a couple of hundreds of thousands transactions per month, which is a couple of cents).

SQL Azure - the cluster uses a server with one database (other than the master), which is either 1 or 5 gb (depends on the technique of deployment). You will pay for those databases as you pay for other SQL Azure databases.

Of course if your client is outside the cloud, you will also be billed for download bandwidth of getting result from the cloud (upload of data is free in azure)