https://wiki.openstreetmap.org/wiki/Tag:natural=bay says:
"There is currently no definitive rule if small islands within a bay should be mapped as part of the bay or if they should be excluded of the bay area as inner rings of the corresponding multipolygon relation."
Hence, I doubt we will get a good "answer" here. I can think of pro and con for each solution. I think this question should rather be discussed in the forum [forum or mailing list or wiki talk page.page](https://wiki.openstreetmap.org/wiki/Contact_channels). If you take this discussion elsewhere, please mention a link here.