I'm on Linux and using JACK too and changing the settings SHOULDN'T haven't an effect on audible frequency, particularly with the oscillators. In fact, it seems like Pd ignores any sample rate I try to set and just takes JACK's sample rate (but perhaps this is changeable with command line parameters). Anyways, I'm not hearing any difference in audible frequency from my own tests, as should be the case.
Anyways, [osc~] uses a lookup table for the sinusoid, meaning there's a cosine wave that's precalculated in Pd's guts and [osc~] searches for the value of cosine it needs with this table (with some interpolation as needed if it wants something in between stored values). A higher sampling rate just means that [osc~] looks up values more often, 48k times a second versus 44.1k times a second. [osc~ 440] in 44.1k and 48k is still going to be 440 Hz, no matter what the sampling rate. Now if you try to play a sound file encoded at 44.1k at 48k, well, that's going to sound different because it's not meant to be read through that fast so everything is going to sound higher-pitched than normal. It's exactly like playing a 33 1/3 RPM at 45 RPM.
You don't really need to worry about different sample rates when using stuff like [osc~] or even [readsf~] at least in terms of audible frequencies, Pd takes care of that. Now when you're indexing into an array with [tabread4~] to play sounds, well, then you need to take sample rates into consideration.