Had the same issue.
I also had the same issue. It looks like instead of reducing the cooldown, buying the second upgrade dramatically increases the cooldown. If you wait around for a bit after buying then the fishing rod reappears but it seems to make it go from a few seconds to about 30 seconds between clicks. I also tried refreshing the page which reset the save, but the same issue happened again after buying that upgrade.
OMG, I found the issue, is about how the decimals are codified in the upgrades. In Spain we use the comma(,) to separate the decimals, and it's what I'm using, but with the English language the standard separator is the dot(.). Tomorrow I will update the code to solve these things.
Thanks for the comments