For the most part, yes. Most holster manufacturers are aware of the slide differences between the 9mm and .40 Auto versions, and have designed their holsters to fit the latter, meaning that they will effectively fit both. Blade-Tech, in particular, is still molding their holsters based on the 9mm P99, which means that they will not fit the .40 Auto version. When ordering a holster, you should ask the holster manufacturer whether they are aware of the slide differences between the 9mm and .40 Auto versions, and which is used to mold their holsters.
Note that Sidearmor is now producing their fine Kydex holsters for the Walther P99, starting with a right-handed IWB (Inside the Waist Band) holster, and will soon follow with a right-handed OWB Modular holster. Two photos of the IWB holster are below:
The first batch of the Sidearmor IWB holsters for the Walther P99, which consisted of thirty or so holsters, were given special engraving, as shown in the following photo:
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