1. I don't understand how removing unused apps would save you money (apart from premium apps like ES or ITSI, but here you should know already if your company is using them). There is a small number of paid apps for Splunk but they are - if I remember correctly - typically associated with particular input types so you need them if you ingest data of given kind.
2. An app upgrade typically (if the app is properly written) just boils down to deploying a new version of an app. The new app version should contain new default files but should leave your local settings untouched. But.
3. There might be some apps which introduce some incompatibilities across versions and need additional things to be done after upgrade. To find out what those are you need to check the app's docs. There is no other way.
4. The method of deploying new versions of your apps will greatly depend on your environment architecture - whether you use clustering on your search-heads and indexers, if you push apps from deployment server, what push mode do you use on your SHC deployer (if applicable).
This might be as easy as going to the apps menu and clicking "upgrade" a few times, but can be much more complicated.
EDIT: Sorry, I didn't notice you posted this in the Cloud section. In this case the "main" part should be easier (but if there are apps manually added - not from splunkbase), you'd need to go through vetting new versions again.
But you'll need to upgrade apps on DS/HFs/UFs as well which _probably_ (unless you manage everything by hand) means uploading new versions to the DS and letting the clients download and deploy it.
