Wild animals die from a variety of causes, many of which would not be transmissable or likely to be an exposure risk to you or your pets. Non-disease causes such as heat, exposure to toxicants/pesticides or food (e.g., insects for the bats) contaminated by poisons, collisions with cars or structures, an initially-survived encounter with a predator, etc., can all result in an unexplained (to us) mortality. You asked about diseases: Yes, there are always diseases circulating, along with internal and external parasites, but generally the prevalence is low in the populations so we don't see individual animals suffering the effects or mortality from that. Once prevalence builds up (more animals carrying or suffering intense effects), or there's a major stress event that makes animals more vulnerable, we tend to see more animals lost to a given cause. There is a bat-specific, non-native fungus-caused disease (white nose syndrome) that is of great concern for survival of bats (individuals, populations, and species-sustainability), so Oregon is monitoring for that: Thus far, to my knowledge, we have not had cases - Washington has however. Skunks are one mammal species that is known for cyclic population outbreaks of a couple diseases, but in truth, most juvenile animals don't survive their youth - thus why litter size is high in prey animals. There could be myriad causes of a young skunk's death that would not be a sign of concern for human or pet health.
The number of bats involved in the mortality event however, is of concern. Given your geographic location, I would be surprised if you're seeing a white-nose event, but just in case, please use the reporting system to get your bat deaths into the dataset, just in case:    https://www.dfw.state.or.us/wildlife/health_program/WNS/reporting.asp
I would also contact your District Biologist asap - They may want to investigate further and may give you some safe-handling guidelines to collect (fresh) any additional bats that die. Call ODFW HQ <personal data hidden> | Toll Free: 800-720-ODFW and provide your property's address so they can give you contact information for the closest District bio. 
Thank you for reaching out - I hope this information is helpful.