This question is only tangential to Bioconductor, as the made4 package uses the CRAN ade4 package internally. So one could argue that it is better asked on R-help.

That said, you need to read and understand the help page for the functions you are using. In the help page for dudi.pca() it says:

Value:
Returns a list of classes ‘pca’ and ‘dudi’ (see dudi) containing
the used information for computing the principal component
analysis :
tab: the data frame to be analyzed depending of the transformation
arguments (center and scale)
cw: the column weights
lw: the row weights
eig: the eigenvalues
rank: the rank of the analyzed matrice
nf: the number of kept factors
c1: the column normed scores i.e. the principal axes
l1: the row normed scores
co: the column coordinates
li: the row coordinates i.e. the principal components

So if you use scatterplot(), you get a PCA plot. If you directly plot pca_$co, you do not because you aren't plotting the principal components.