I can't find any official word on it, but the idea the Shrek borrowed heavily from the plot of Ladyhawke is not uncommon.
e.g.: From this review:
At least when Shrek half-inched the plot, it was consistent throughout.
(Half-inched: British slang; pinched, or stolen)
IMDB also includes Shrek under the "Spoofed in" connection section for Ladyhawke.
And in the book 100 Animated Feature Films by Andrew Osmond also draws a link between the two, saying:
... the loose later scenes become a star-crossed, shape-changing romance, echoing the live-action Ladyhawke (1985), and, more overtly, Disney's Beauty and the Beast.
While there appears to be popular opinion that Shrek at least referenced Ladyhawke, I'm unable to find any official word about whether Fiona was an intentional parody.
Finally, the book on which Shrek is based is called Shrek!, and was written in 1990, five years after Ladyhawke. Again, there's no indication that the book deliberately parodies Ladyhawke.