I could see why they'd nerf the Ninja Squid swim speed for the same reason you just stated. Another thing to note is that with Ninja Squid in its current form, people can still make the center gap jump in Urchin Underpass just fine, but the nerf will make it much harder to jump across. So common jumps that people can make might be harder for those with Ninja Squid. Also, I don't know if the comparison between Ninja Squid and Cold Blooded is a proper comparison. Although Cold Blooded may be better, it's the most situational ability out of all the others. Every ability in the game can activate almost all the time in battle, but Cold Blooded is not like that since it needs a couple requirements.
First off, the opposing team needs to have at least one member with an Echolocator or a Point Sensor (which is very rare in my eyes since it's tied to some of the lesser used weapons - like the Classic Squiffer and Forge Splatter Shot Pro). Secondly, Cold Blooded can only work once the enemy has their Echolocator special filled up, so that's a lot of time waiting for Cold Blooded to activate (and even longer if the enemy decides to hold on to their Echolocator).
If those two requirements aren't met, then you've wasted an entire main ability for the whole duration of the entire match.