I worked IT for JPL's Cleanroom Group a few years ago. Biological contaminants are only one factor. 95-99% of the cleanrooms they have are not much cleaner than something like a typical elementary classroom with a well kept air filtration system (not great). These are Class 100K rooms [1]. Less than 100K particles of 0.1 um size or bigger per m^3 of air (dust, hair, skin, anything really). Offenders of contaminating the rooms some brought in unapproved or contaminated materials, like non-cleanroom notepads or gaseous/non-cleanroom markers/pens, cardboard. The reason why the rooms were not operated cleaner is because of their size. Some were large like 40m by 40m by 40m (the main Spacecraft Assembly Facility where the Herschel instrument saw final assembly), others housed special capabilities like the 25-foot Space Simulator [2], shakers and bakers (rotation/vibration test pedestals, and space vacuum hot/cold chambers), or isolation pads (pedestals mounted on ultra heavy 40'x40'x40' blocks of concrete to reduce vibration for optics instrument testing). It was also common practice to certify a room at one level, and operate it like it was the next higher level with minimal cost and maximal benefit. Things like additional air exchanges, daily or twice daily cleanings (instead of weekly), extra HEPA filters, stricter ESD operations, stricter temperature and humidity control (ESD & Planetary Protection reasons). This was often more than sufficient to appease the Principal Investigators, Instrument Designers, and Planetary Protection.
Many rooms were Class 10K capable. A few were Class 1K or Class 100 capable. But those were very small rooms, sometimes even 10'x10'x10' tents setup in a one level less capable room. Only two rooms operated were even capable of operating at Class 100, IIRC, and only did so when necessary. There were apart of chip fabrication building.
To answer your question, Herschel has its base requirements similar to anything we send off into space, and then it had it optics instruments requirements. Projects have been ruined when instruments do not work or do not work as well as designed because of dust, ESD, or a hair particle. It's really hard/expensive to wipe your lens with a microfiber cloth in space; JPL once did a study to determine the cost/feasibility. It dwarfed the original project.
[1] http://en.wikipedia.org/wiki/Cleanroom#ISO_14644-1_cleanroom...
[2] http://www.universetoday.com/97249/jpls-torture-chamber-for-...