Enclosure will protect printer from dust and it will also keep the ambient temperature more stable. Dont make it hermetic sealed, better add few holes on the front and few on the back for example. I have a low rpm fan with dust filter because I mostly print PLA and in long prints (12h+) temperature can go a bit too high if there is no airflow at all. Keep in mind that enclosure should be removed sometimes for mintainance, removable sides is what you should look for.

You can leave filament on the printer, but if you dont use it for a long time it could get wet and then you have to dry it. Keep the rest of the spools in plastic sealed box or bag and put some silica gel inside.

Full calibration should be done once, but fine tuning when you face some issues or when you change to different brand or filament type. It depends how well the printer is assembled and how experienced you are, it can take only 5 min every few months, but begginers can spend days sometimes.

Extra tips: clean your rails and wheels whenever you can (once a month at least) for dusty garage. Get a kitchen sponge, drill a hole in it and guide filament trough the hole to remove any dust before extruder.

Welcome to the most fun hoby and happy printing!

1. Keeping dust and debris out of it while not in use is a good idea. However, if you are printing in low temperature materials such as PLA, TPU, and probably also PETG you should not run your printer in an enclosed box. The heated bed plus the waste heat generated by the hot end, etc. in a sealed environment can eventually become enough to soften the filament while it's still in the feed path, which will cause problems. Your PLA prints will also get saggy and noodly if the air temperature inside the box remains elevated above the material's glass transition temperature for any significant length of time. (The peanut gallery can argue in the comments just how high the temperature needs to be, but it's better to just not risk it.)

1a. This is not applicable to high temperature materials such as ABS, polycarbonate, or nylon/PA. For these materials you will probably need to run the printer in an enclosure to maintain a stable air temperature, but you probably won't be messing with these materials soon... or ever.

2. When not in use you should store your filament in an airtight box, by preference with some manner of desiccant in there with it. Silica gel is what most people use. The reason being, all polymers are hygroscopic -- that is, they absorb moisture from the air -- and moisture in your filament will alter its physical properties making it more brittle and less flexible. "Wet" PLA tends to snap without provocation... including in the middle of a print job. Also, moisture in your filament will be boiled off inside the printer's hotend and essentially cause the extruded material to froth and foam which will produce lousy print quality or even outright print failures eventually.

2a. It's also a good idea to invest in a heated filament dryer, or jerry rig your own. This will allow you to drive moisture out of spools of filament that have absorbed moderate amounts of moisture to revive it, and is outright necessary for some super hygroscopic materials such as, again, nylon.

3. Any time you change the nozzle, do anything that might alter the thickness of the build plate (adding kapton tape to it, for instance), change out the build plate for a different one, mess with your belt tension, undo any of the hardware that mounts the hot end/gantry or anything attached to it such as a z offset sensor (if you have one), crash your nozzle into the bed due to manual operation error or g-code fuckup, or if you notice any first layer adhesion problems or any other mystery print quality issues that don't appear to have any other cause.

I will not reiterate the great things others have said but I've used old windows to create an enclosure for my printer and it definitely helps with the prints. Also since you're a new user and have an Ender 3, I would recommend you to take a look at thingiverse.com and printables.com - if not already done - for great tweaks to protect your printer but also to find great things to print.

For your printer, you may be interested in cable guides, filament guide, spool roller, fan duct, bed lock (they will keep your bed in place so you will not have to deal with bed tramming anymore before your bed leveling sessions)...

Finally, although a little bit off topic, if you get bored to walk to your printer to watch the prints and would like to add some level of safety in case anything goes wrong I would highly recommend considering octoprint.