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After removing unconnected via pads and repuring copper fill, the clearance between the via hole and the fill will be defined by the rules, but the pours will be closer to the hole. Does this bring risk when manufacturing vias, especially when drilling?

Clarification: Yes, the only guide in this case (as well as many other when making PCB) is to follow PCB manufacturer's guidelines. What made confusion in my case is that the rule which defines clearance between any hole and copper was wrong, so when I remove via unused via pads, the copper comes to close to the hole (DRC was not complaining due to the bad rule).

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As long as you stick to the PCB manufacturer's design rules, I don't see a problem.

Good values for these rules can be found here

You may also have a look at: Vias without annular ring on internal layers, non-functional pads in a via

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