When I play a D scale (on my D whistle) it sounds right to play a C#
When I play a G scale (on my D whistle) it sounds right to play a C
When I play an A scale(on my D whistle) it sounds right to play a C#
Is this correct?
Yep!
D major scale has F# and C#
G major scale has F# and Cnat
A major scale has F#, G# and C#
Assuming we’re specifically talking about major scales, yes. dorian, mixolydian, and minor scales will be different.
Thank you! 
Yes, for ordinary Major scales.
But ITM has a feature that Breandan Breathnach called “inflection” where, on D pipes, flutes, and whistles the notes C and F tend to fluctuate between natural and sharp.
It is so, in the version of Banish Misfortune that I learned many years ago, and in many other tunes I’ve learned since.
Inflection is, in fact, inherent in the old church modes which are used for much of ITM. The note B can be ‘inflected’ at times as well. IIRC, those are the only three notes affected by this feature of modal music.
Thank you!
Breandan Breathnach writes (keep in mind he is assuming the usual D whistle/flute/uilleann chanter)
"No reference has been made to accidentals…two such notes occur, C# and F natural.
C# usually occurs by way of variation and almost invariably in a weak or unaccented position…
F natural on the other hand occurs only in the accented position."
In uilleann piping C fluctuates constantly and by context.
There’s a stereotypical uilleann motif dcA in which c is nearly always sharp and often staccato.
There’s another common motif ABc where c is nearly always natural and legato, and often slid into.
It’s why you hear people say that it’s C# coming down and C nat going up.
Breathnach also wrote (in the introduction to CRE1):
The two notes C and F are also exceptional in another way: they are somewhat sharper than the corresponding notes on the piano. It’s said that directly halfway between B and D on that instrument lies the C natural of traditional music, i.e., pipers and fiddlers would play C a quarter note higher than on the piano. This may be the reason why C# is so often played for C-natural by the box-player. In a slide up from E to F# the traditional fiddler makes F-natural, so that this is not a fixed note. For this reason I didn’t use the ordinary sign to indicate it but used instead an asterisk. Generally, it’s better to play F# on the piano or box.
to explain how he indicated these notes in his collection(s), with an *.
It’s probably best not to get too attached to set values for particular notes, as Richard said, things can fluctuate according to context (and I would extend that beyond the C), different instruments (and styles ) may vary in their approaches so it’s always good to be flexible and adapt to your surroundings. And that’s before we even touch on the expressiveness of the ‘in between’ notes.
Yes, very good point, thank you
Interesting what he says about the pitch of C natural.
Assuming we’re talking D uilleann pipes, C natural is the flat 7th over the drones.
Highland pipe harmonics and tunings have been poked and prodded more than most, and one of the interesting things to come out of all the study is that there have been a number of tunings for the note in question (what would be C natural on D pipes) each having a distinctly different effect, and the fashion for these tunings has changed over the years.
What has never been in fashion with Highland pipers is the Equal Temperament note, 1000 cents above tonic.
The old note was a bit sharp of ET, 1018 cents above tonic (9/5) which can be heard in recordings from the early 20th century up through the 1960s. That’s the Just Intonation tuning of the flat 7th. This tuning of the flat 7th has a heroic, calling effect not unlike a hunting horn.
For the last half-century or so the popular pitch has been over a quartertone flat of ET, 969 cents above tonic (7/4). That’s the flat 7th in traditional Blues and in numerous folk tunings including in India. This tuning of the flat 7th has a sweet smooth bluesy effect.
I do wonder what specific pitch Breathnach is referring to.
I know that myself, due to needing to have C natural right in tune to ET (because of the nature of some of my gigs) I can keep my upper-hand index finger near the hole to “shade” the C and give that sweet effect heard on the Highland pipes.