The starred channel option is a great way to separate the channels you use the most from the pack - in essence, starring a channel places it into a list of channels above your regular list. Conversely, muting channels that you want to be in but would like to avoid having as a distraction is a great practice, and places them at the bottom of your regular chhanel list.
Another little trick - Hubspot lists channels in alphabetical order. Every so often, we want a channel to remain at the top/bottom of the pack without starring or muting.. so we throw an " a- " or " z- " in front of the channel name so it appears in the desired spot on the list.

As for team organization within channels - our rule of thumb: if more than 4 people are needed for a chat or if there are external stakeholders (guests) needed for the chat, we use channels. Otherwise, we roll with direct group messages.

Our team and number of channels at Capiche right now are low enough that simple names like #growth or #front-end are enough to help us find the channels we need.

At Zapier with hundreds of channels, the trick was to add function-based prefixes to channels, including #fun- for non-work discussions such as #fun-cooking, #city- for location-based discussions for teams in the same area to plan meetups, #team- replaced with the team name for work channels such as #marketing-writing for a marketing team channel about writing. It gets a bit tedious to maintain, but makes it easier to skim through a wide number of channels and find what you're looking for.