Running heating pipe through beam under floorboard?
Go through the centre of the joist with the hole.
This means any future nails from either side are less likely to puncture the pipe.
Also the stress on the joist is zero at the centreline. But a maximum at each edge.
And I have seen people run pipes and wires like you suggest - fine for them but later owners trying to reduce squeaks or moving boards then have nasty consequences...
I spent weeks trying to locate why a circuit breaker kept blowing. Eventually found a nail through a floorboard into a wire that went over a notched joist just like you plan. The names I called the person that did that - if I had met them at that moment...