[Feature]: Refactor to reduce code complexity

[rly]

What would you like to see added to HDMF?

Some functions have high cyclomatic complexity and are therefore more challenging to understand and maintain. See NeurodataWithoutBorders/pynwb#191

We currently use # noqa: C901 to make the functions pass the flake8/ruff C901 check.
https://github.com/search?q=repo%3Ahdmf-dev%2Fhdmf%20C901&type=code

What solution would you like?

Refactor the functions into smaller ones or use less branching/complexity in those functions.

Do you have any interest in helping implement the feature?

No.

[rly]

This is low priority, but I wanted to flag it as tech debt that would be good for us to resolve and I think it would not be too challenging.