Without a doubt, but the ROC would also do its utmost to shield its "trump cards" from the initial bombardment by way of hiding them in caves/tunnels (à la Iran) or distributing them sparsely throughout the countryside (making it more difficult for PLA forces to find/track/destroy them). This would almost mirror the "Scud-hunting" phases of the Gulf War, although in this scenario the area is much smaller and the weapons much more potent.
I agree that missile systems need to be evaluated as part of a whole rather than a standalone component, but how capable a particular missile system is can certainly change the calculus of the overall campaign, even with ancillary platforms (SAMs, radars, etc etc) taken into account.
The Yun Feng's greatest advantage is its speed. The missile itself might be quite visible on radar and easy to track, but whether or not the PLA can detect the target, track it, launch interceptors, and get a kill in time is another question.
I'd imagine that the PLA have exercised this scenario with their own CJ-100 missile, which should be similar to the Yun Feng in terms of flight profile and kinematics.
These are alleged photos of its transporter vehicle:
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It's a big missile, certainly larger than the CJ-100 and almost DF-26 sized (or even bigger). Not sure how much space the actual missile (or missiles) is taking up, but it is without a doubt that this would be the biggest threat to China in a hypothetical Taiwan operation.
The proximity of China to Taiwan works both ways; it gives China the ability to rapidly track and target military assets in Taiwan but it also gives the latter the ability to hit back with short reaction times.
And no, there is no scenario in which China involves nuclear weapons in such an operation.