Theme structure for multi-site
If they only differ in color, you should provide a theme setting for choosing it and setup the theme in /themes/custom/mymulticolortheme, so it will become available for all sites. Otherwise you have to maintain multiple nearly identical themes, which is a time killer when you have to fix a bug or add a feature.

If you have different themes for each site you should place each theme in the particular site theme folder like /sites/site1/themes/custom/myspecialthemeforsite1, /sites/site2/themes/custom/mytotalydifferentthemeforsite2 etc., so that they are only available for sites they belong to.