Yes, Stink Bombs inflict "normal bomb damage", which means they still do their splash damage as well.  Precise Bombs will limit who takes the splash damage, but the fog cloud / stinking cloud spell still cover their [normal area](http://www.d20pfsrd.com/classes/base-classes/alchemist/discoveries/paizo---alchemist-discoveries/smoke-bomb).  The Fort save DC is [determined as normal](http://www.d20pfsrd.com/classes/base-classes/alchemist#TOC-Discovery-Su-),  

>10 + 1/2 the alchemist's level + the alchemist's Intelligence modifier

per the PFSRD.