There may not have been any concerns at the time, but the damage to the reputation is real, albeit difficult to measure. Nevertheless, you can see that Windows only ever seems to lose market share. Windows desktop is shrinking, Windows mobile is dead, Windows embedded is phasing out, and Windows server is only used for the bare necessities. You can argue that Microsoft successfully managed to pivot to cloud, but that is a rather shallow moat.
Among all other variables affecting the market share of Windows, the effect of the inscrutability of the Win32 API is almost certainly negligible. Especially given that as far as I know, their APIs designed in the past 20 years haven't typically been as horrible.
