Multivariate analysis

I need a basic answer regarding the data matrix used in multivariate analysis.
It contains data of sample spots, which are categorical variables, species, and their abundance on a given scale (1-5), at each given location. What kind of data are species in this case - also categorical, but their abundance is ordinal?
What are your experiences regarding missing values - if I don't have a species present on one location, do I give it a zero or make another number, since PAST won't do PCA analysis with missing data?

Thank you in advance for your answers.
If your dependent variable is abundance, e.g. the number of snails at a sample spot. Then you can count the number of snails 0, 1, 2, 3, ...

An zero is also a number, not a missing value. (And the number of snails is a ratio variable). The number of snail can be classified on a 1 to 5 scale. A zero number of snails would then be classified as "1" on the 1 to 5 scale.