As an ISV we are planning to update the API version of our package metadata components to v.50, so all of them will have the same. My question is:
Can we (and would want to) upgrade API versions of non-upgradeable component like email templates?
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Yes you should be fine upgrading the versions to the required version in your packaging org or in your metadata!
There won't be any duplicates in the subscriber org on package installation and they will ignored! This applies for all the components that days upgradable false in this document.
Let's consider an example, let's say you package up the page layouts and upon installation these page layouts are in subscriber org!
Next package, you have modified certain items in your package layout! Upon package upgrades in subscriber orgs, you will notice that package layouts are not upgraded! They are simply ignored!
Same with email templates,unless you package up a new set of templates! A version upgrade has no effects!