Is there a best practice storing Process Builder in VCS(Git)?
Ideally? Don't deploy Processes or Flows (same metadata type) to persistent orgs via Continuous Integration, because you will hit the limit sooner or later. If you use scratch orgs, they won't be affected, but the persistent org that is your metadata's ultimate destination will be.
If you are a Salesforce end user, you can probably fix the issue just by deleting old Flow versions (although there isn't a definite way to stop them from accumulating in the first place).
If you are an ISV using a 1GP packaging org, you won't be able to delete Flow versions that have been packaged, making this issue extremely serious for users of CI/CD. Additionally, each managed package version that's installed by your subscribers containing a new Flow versions accrues that version in their org, so 50 total upgrades will result in a non-upgradeable subscriber org.
I've discussed this issue with the Flow PM and engineering team (I work on managed packages at Salesforce.org) and they are evaluating ways to address it in the future (safe harbor, no timeline available at present).