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Do they still affect reputation score in Peakd?

Yes, exactly as they do on Ecency were those downvotes have always been added at the bottom of the vote list.

Does rep score even matter any more?

Such small downvotes are not going to affect reputation either way.

Upvotes are unaffected, downvotes are only affected in that the ui doesn't show them, they still count at the blockchain the same as before.

This is simply about silencing a few trolls.

Reputation never really mattered because all it measures is how much stake has voted for you.

This is very much a pay to play system unfortunately.

Depending on how fast you want to climb the ladder.
Many people pay nothing but their time and have done very well.
It just depends on if the large stakeholders support your content, or not.