SponsorBlock – Skip over sponsorship segments on YouTube

For these sponsored contents it doesn't really matter though. The content creator has already been paid, so whether you watch the segment or not, they won't lose or make money.

They will if the practice becomes common place. Advertisers will know what percentage are just skipping automatically and reprice the spots value accordingly.

That's not true. Many get money based on how many clicks an affiliate link gets or how much an offer code is used. At the minimum this data is used to determine if the company decides to continue buying ads from the creator.

I could see it escalate into an arms race: if the new norm for watching videos will be to automatically skip sponsored segments by some popular software, the sponsorship offers will either dry up, or the resulting sponsorships will be designed to be more difficult to skip (eg. by making content creators incorporate them throughout the video in many small chunks, or as overlaid audio/video, ...).

Similar to what happened to web ads in communities that tend to run adblockers: more and more obnoxious advertising (intersitial ads, animated ads, etc.), advertising incorporated into content (ads-as-content like on Reddit), cross-site tracking and retargeting.

I tend to manually skip sponsored segments (especially for snake oil like VPN services!), but I'm not sure if writing automated software for this is the right thing to do in the long term.

That's a too simplistic view and not how sponsorships work. The sponsor expects a return on the investment. If a sponsorship does not generate revenue, that content creator will stop getting sponsorships because their audience is worthless.