Yes, you can load test cloud applications. Whether they're on-premise or cloud hosted the applications are accessed with HTTPS protocol. You may need to ensure the servers you run JMeter on have network connectivity to the URL of your cloud applications.
One point to consider is the location of the JMeter servers. For example, if you load test a cloud application hosted in a US-region and your JMeter servers are in a datacenter in another part of the world there will be latency between the servers measured in your JMeter response times. Ideally, the JMeter servers should be located in an area that is representative of where your real users will be.