Neither San Francisco nor Segoe are at all similar to Helvetica. Apple used Helvetica as the iOS system typeface for years before switching to SF, so I don’t think the licensing cost is the main issue.
Had it licensed from Linotype since the very early 1980s I think? It's literally one of the reasons for the Helvetica's cachet, Linotype were clever with their licences (Apple, Adobe, Xerox & it's a core postscript font).
Also, Helvetica clones exist mainly to get around licencing costs related to physical printers (if your software uses something metrically identical you can just use the existing postscript drivers). SF and Segoe are for UI text, which Helvetica is not suited to (Apple had to adjust the metrics to make it more usable, for example)
