Everything in SharePoint, including navigation, is security trimmed, meaning Microsoft is analyzing permissions in real time before displaying that element on a page for a given user. Therefore, if you have a lot of unique permissions (broken inheritance) or a large or complicated navigation (global or quick launch) you may start to experience issues. If there is a general slowdown, you will also be the first to experience more significant delays.
Microsoft does not recommend structural navigation for SharePoint Online although it is the default setting. If you routinely have issues, this should be the first thing you tackle: https://docs.microsoft.com/en-us/office365/enterprise/navigation-options-for-sharepoint-online
If you routinely experience issues with your site, you may be asked to make this change.
To review all of the access, including granular ones down to individual files, in a site, you can request a permissions matrix report.