Actually the HEPA Vacuum has to do with the size of the offending particulate in the guano. The HEPA vacuum in order to be a real HEPA vacuum, needs to be 99.97% effective for particulate down to 0.3 microns in diameter. This is extremely important to avoid further contamination of the building you are working in as well as reducing and even preventing exposure to yourself and those around you.
When working with guano, pigeon poop and rodent droppings, it is also important to be wearing the appropriate respirator with the proper filters.
P-100's are typically what you are looking for in these situations ( that is the NIOSH HEPA rating for respirator filters). You also need to be thinking chemical exposure if you are using disinfectants (P-100s don't filter out chemicals) and eye protection, bacteria and viruses (such as Hantavirus) can enter through the eyes.
I have worked in Environmental and Occupational Health and Safety here in Canada for 23 years dealing with asbestos, mercury, lead, PCB's, guano and Hantavirus, These things are nothing to take lightly.
Try cleaning up drywall dust with your wife's household vacuum and you quickly see what I am talking about. The dust from sanding dow drywall is so small it will blow right through a standard vacuum filter, but will not go through a HEPA vacuum filter.
