The MISA account is a freebee that you can get with the CBAs standard variable rate loan. It doesn't cost you any extra, so there's no fees to deduct specifically for the MISA account.
For example, you can have a standard variable loan outside of the CBAs professional package, currently 6.15% with fees of $8 per month, and get a MISA account for nothing extra, and no annual fee.
The CBA professional package fee (currently $375) is used as an annual fee covering any loan accounts under it.
If the only loans you've got with the CBA are for personal use (such as your PPOR), then the $375 fee wouldn't be deductable because the loans aren't for deductable purposes.
If you've got a PPOR loan and loans used to purchase IPs, then it's likely at least part of the $375 annual fee is for deducable purposes, so you should be able to deduct at least some of the fee.
I'm not an accountant but my expectation would be that the annual fee of a professional package with most lenders is deductable based on the use of the loans within that package, no the use of the optional extras such as offset accounts, credit cards, etc.
The MISA account would generally be irrelevant to the deductability for the annual fee because it can be argued that the fee is not actually for the MISA account, it's for the lending package.