Will placing a copper polygon/zone over multiple (same-net) surface-mount (SMT) pin-pads create any thermal issues with the solder (for example, paste not sufficiently heating up)?
The solder mask will still keep individual pins separate, where there is sufficient pin-to-pin clearance (pin pitch).
For example, pins 48 and 49:
It really depends on the thermal mass of the devices and the soldering process - there are various variations on the manual soldering process, typically involving various modes of preheating the board, components, and use of fluxes, vs IR reflow, vs vapor phase reflow.
I have used large solid copper pours with dense power converter designs, and they posed no problems. I evaluated the behavior of the board during vapor phase reflow by instrumenting it with thermocouples and not much was different compared to the same board, same components, but a layout with thermal reliefs for all the pads connected to copper pours (polygons). But that's just an anecdote, it the your mileage may and WILL vary caveat emptor very much applies!
There's plenty of circumstances where it would be problematic. So you will have to talk to your PCB assembly house in detail to make sure it's acceptable. They are the ones that will ultimately know (or are expected to know, at least). It really is process-specific, and even though PCB assembly sounds like a "single" concept, there's a lot of detail in how it's implemented on assembly lines, how the process parameters are set, etc.
