It is standard procedure, but some searches are more thorough than others, which is why cops are occasionally killed by suspects with guns they failed to find. A Mexican illegal was executed recently for just such a crime. I think it's a mix of respect for personal privacy and not wanting to probe too closely at the potentially stinky bits of a suspect's anatomy.
Cops should use one of those metal detecting wands that security guards have. I wouldn’t want to go anywhere near the stinky bits of a perp’s anatomy but potentially getting killed over an insufficient search is also not an option.