An appoggiatura in Baroque music often represents a note held over from a previous chord, a dissonance that clouds the chord and then is resolved. Writing each note as equals would imply that they should take the same amount of time. An appoggiatura typically puts emphasis on the first note, and the two may not be the same length.
See, for example, La Sylva (on pg. 37 of this document). The piece is slow and regretful, with nothing lining up precisely on the beat. The appoggiaturas emphasize the regretful and slightly chaotic nature of the music. Perhaps Sylva was a lovely lady who got away, or a good friend who died.
If you are ever concerned that ornamentation was added later by an editor . . . get a better edition. While ornamentation should typically be left out when first learning a piece, in Baroque music is it essential to the overall artistic nature of the piece and should not be left out in performance. See, for example, the way these folks decorated their churches:
There's lots of physical ornamentation. Chipping St. Teresa and her stone columns and arch out of this alcove would leave a perfectly functional church, but it wouldn't be very Baroque. Likewise, removing ornamentation would alter the style of the music.
Finally, Baroque music has a strong tradition of improvisation, as exemplified in continuo playing and improvisational patterns like La Follia. Writing the two notes as an appoggiatura leaves room for the performer to vary the length of each of the two notes depending on the audience, the performing space, and the individual tastes of the performer.