I would like to know how to pronounce the Latin word Ducissa- should
it be doo-kays-uh, doo-keys-uh, doo-kess-uh, doo-chess-uh... and on
which syllable should the emphasis be placed?

Why not  "do kiss uh" with the accent on the second syllable?

If Ducissa is Italian, as I believe it also is, I would say  "do chis
sa" with the accent on the first syllable.

That ought to get some correcting comments.  ;)

The problem is that there is no standard way of pronouncing Latin. The
word is (I think) a medieval-Latin word meaning "duchess" so the
classical Latin pronunciation doo-KISS-a would not be appropriate in
that the word didn't exist in classical Latin. In the Middle Ages each
European country had its own way of pronouncing Latin.

I would suggest you either pronounce it the modern ecclesiastical way
doo-CHISS-a or the Anglicized way doo-SISS-a.

However you pronounce it, the accent is on the second syllable.

Spurred on by Mforster, I actually looked around a little.  Ducissa
was a latin word for duchess used in the 10th century, obviously a
female form of Dux.
In light of the fact that Italian for duchess is duchessa,  du KESS a, 
I now think the older word would also have been similarly pronounced:  du KISS a.

That's the issue I was having- I was trying to figure out the rules by
looking through Latin dictionaries and guides, but there are so many
interpretations!

I did find out that it's Medieval Latin so it could probably be
pronounced doo-CHISS-a or doo-KISS-a.

I'm considering using the name for a women's jewelry company, so I
wanted a proper pronunciation. If there's no standard, then I guess no
one can correct me! :)

In that case, I would ask a variety of people how they would pronounce
Ducissa (without giving them any prior information) and go with the
majority, hopefully a large majority.  If you are establishing your
new company, you don't want to be having to correct customers on their
pronunciation, even if you know that it is historically incorrect.  If
someone pronounces it correctly in this situation, you can either just
go along with his/her pronunciation; if they point out that your
choice is incorrect, you can compliment them by agreeing and explain
your choice.

Now what do the higher authorities have to say?  :)