I think only suiteapps would use a suiteapp, so that would mean account customization for individual customers
folder structure for code, i think depends on how many scripts they have, I've seen everything just get dumped in /suitescripts/ which is fine if there's only like 10 script files, but it gets silly fast
I think generally people use a folder structure based on solutions
I have seen them organized by script type, which... i personally don't think it brings much to the table... we use naming conventions that have the script type in the file name so there's never any need for them to be in their own type folders.
git as a repo i think is pretty standard
for deployments you can just modify the deploy.xml to only deploy the objects/scripts you need.
there's certainly more that can be done with deployment pipelines and integrations to Jira (and its ilk) but I don't think they're essential