Yes they were both uploaded into a single image but separated into two hard drives.
1- What happens when I try to deploy that image to a computer with only one HDD ?
Images are always deployed in the order they are listed in the schema. Images->search->view->schema. If the original image uploaded more hard drives than the destination has, it will just deploy in that order. Example: The destination computer has 1 hard drive but the image has 2 hard drives, the hard drive in the destination computer will receive the first hard drive image listed in the image schema. The second hd listed in the image schema is just ignored. Additionally in your image profile->deploy options you could change the order if you wanted the second hd to deploy first.
2- Does this mean If I intend to clone one HDD (or restore one HDD), I should always unplug any unwanted HDD that resizes inside the computer before uploading/deploying?
There are multiple ways to handle this. First you could just let both hd's upload, then in the image profile you can turn off the 2nd hd. Then it will never deploy. Second, you upload only the hard drive you want. In the image profile upload options select upload image schema only, then upload the computer. It won't upload any data, just the schema. Back in the image profile->upload options, uncheck upload schema only and select use custom upload schema, then you just check the hard drives you want to upload and start another upload task.
Hopefully that makes sense, it can be a little confusing. Finally remember that CloneDeploy is not intended to deploy to any computer where you want to save data even on separate drives. On the client side it always deploys in the order of the drive name such as /dev/sda. Most of the time that should be the OS drive, but what if you data drive was detected as /dev/sda then that drive will be overwritten. This could simply be because the sata cable was plugged in the wrong port or anything else that could impact order.