I think your title is misleading: it should me ‘My problem with samples’ 
There are pros and cons to have both, but a lot more pros to stay in samples. For instance, if you do batch processing of many files, each with various SR, then you would need to be aware of that… so a little pain for a lot of potential freedom is what we do, as usual.
If you stay in 44.1, it is no issue
if you move, it is a larger issue than you say, so you’ll have to be disciplined depending on what you want to do with it.
if you move between CCE, for batch processing, that is even truer.
We have investigated the SC way (in second) and it creates (for me) at least as many issues that way, so we’ll stick with samples, which is the only true measure. If you make a simple division with a simple query (which we have to do in SC the other way round) then it is sorted everywhere for your use case.