Maybe, but it wasn't at all to the same degree. Floppies were verging on uselessness in 1998. Capacities hadn't increased in a decade, while code and data sizes were growing exponentially. Floppies could barely fit anything useful anymore. A wide variety of replacements were available, with Zip, Jazz, Bernoulli, CD-RW, and others all competing. There was no standardization, so the replacements kind of sucked. Removable data storage was just a complete mess at the time, so eliminating the most standardized but vastly least capable option wasn't that big of a deal.

With audio connectors, it's not like that at all. For wired connections, there's one universal standard that works great. There's no analogous situation to being unable to fit your massive bloated Word documents onto a 1.44MB floppy disk. Moving past the floppy disk solved a bunch of serious problems, while moving past the headphone jack isn't solving any problems.