Can I have 2 different backups on the time capsule?

Regardless of where you store your iTunes & Photos libraries on the MacBook Pro or the MacBook Air, Time Machine on each of these notebooks will make a backups of each respective device to your Time Capsule.

If saving space on your MBA is important to you, then you may find the following article helpful:

• How to free up storage space on your Mac - Apple Support

Lets say I copy my pro to my new air

You won't be able to use Time Machine for this, if that is what you are thinking. You must use Migration Assistant on the MacBook Air to transfer the data from a Time Machine backup of the MacBook Pro. More info here:

How to move your content to a new Mac - Apple Supporthttps://support.apple.com/en-us/HT204350

If you have a new MacBook Air, you have free phone support from Apple for 90 days. If you are not familiar with Migration Assistant, I would recommend that you get with a product specialist to walk you through the process step by step over the phone.

Does Time machine then backup separately those 2 MacBooks ?

Yes, as we already noted above. Time Machine will back up everything on a Mac unless you tell it otherwise by using Exclusions in Time Machine Options.

can have 2 different backups on the time capsule?

Yes, assuming that you are asking about Time Machine backups.

Keep in mind that each Mac will only able to "see" the backups made by that particular device. Another way to say the same thing......if you are using the MacBook Pro, you won't be able to "see" the backups made by your MacBook Air. If you are using the MacBook Air, you won't be able to see the backups made by the MacBook Pro.