i'm doing a little research about effects of using and not using pdf compatibility and "use compression" when saving native .ai files.
majority of tutorials says using compression reduces file size but they don't tell what does it actually do, even in guides on adobe website they just say:
Compresses PDF data in the Illustrator file. Using compression increases the time required to save the document, so deselect this option if you’re experiencing very slow (8 to 15 minute) save times.", and actually, using compression reduces file size even if "create PDF compatible file" is turn off, so it affects other than PDF data in the .ai file, if i'm right.
ok so basically just do 'use compression' unless the save times are causing you issues, but really unchecking 'pdf compatible' will do more to speed up save times if thats your issue. The use compression setting is a bit like what a zip file does. its saving the file in a disk space saving manner. it takes a little longer but reduces file sizes. the quality of the file or images is in no way affected. i guess the real world equivalent would be putting things very neatly into a small box, or just chucking them quickly into a large box. all the same stuff is in there, it just takes longer to pack it neatly. and the big box takes up more room in your cupboard/SSD.
the use pdf compatibilty thing is really a bigger difference in file save time, i generally leave it on for simple stuff, as the file preview is is much more useful with it on, and allows placing the document into an indesign doc for exmaple. but on large complicated documents i turn off pdf compatibility until the job is effectively complete, it makes regular saves much much quicker, and the only need for the pdf compatibility is such as when you need to give it to someone else, who may have a different version of ai or be using it placing into another layout, or to get good thumbnail previews. the slow down in file saves is enough to make me turn it off for most large files though, id rather have regular saves.