We're having issues with two customers and one vendor not receiving our emails sent from NS. Are there any known issues with emailing from NS we should consider in troubleshooting this?

Check the bounced list in NS, once an email bounces it stops trying to send to that list. Remove them the bounced list if they are there.

These aren't showing up on the bounced list. NS thinks they were sent but they're not reaching the destination. I suppose they could be getting caught in a spam filter on the recipient end but they do get some of them.

I'm 99% sure it will be on the receiver, a filter, a receiving rule.. Do check you own domain is setup to allow Netsuite to send email on your behalf. https://netsuite.custhelp.com/app/answers/detail/a_id/9427

Yep sounds like something on the mail server blocking rather than the Netsuite side.