Generally we would advise against posting directly to a nominal unless it’s something like bank charges, but it does depend on how you work.
Using an invoice allows you to not only add VAT (if you’re registered), but also allocate it to a client/supplier and find any documents relating to it too, which helps with things like audit trails should HMRC ever query it. Tagging directly to a nominal skips this process and can make it a little bit trickier when you’re trying to cross reference or check things.
You mention about costs per department. I think what may help here is project tags. This allows you to group invoices (sales and purchases) to a “project”, which could very well be a department - they’re pretty flexible.
I’ve included a few links below relating to the projects within QuickFile that may help: