Is there a limit on the number of applications I can protect?

Yes, it depends on ElecKey editions. e.g. ElecKey Professional provides 2 Program IDs. That means, you can basically protect two applications. There is no restriction how you want to use the available Program IDs though. It's possible that you may reuse the same Program ID for two different applications if they would never be installed on the same machine. But, it's a little inconvenience to manage licenses.
It is our pricing model, if you want to protect more applications, you can upgrade your ElecKey license to add more Program IDs to your system. Please see from the link below.
In our system, you can generate unlimited licenses for unlimited copies of your software. And, you get free online technical support with no annual fee.
Other similar products may use a different pricing model. For instance, you can protect many applications as you want, but you have to pay a fee for each copy you license your software. There may also be a charge for subscription or annual fee.
FYI. If you need to use many Program IDs, you may consider ElecKey Ultimate. It provides 4 Program IDs with full features and solutions, at a lot of savings. For instance, you get the Activation Server solution that allows you to automate the process of issuing licenses for your software. Please find more information from the link below.