Apache going to 100%? That's really odd, I've never seen that across the dozen I've maintained over the years. Is there something trying to hit the site hard like one of the many site checkers that run out there, or are you maybe trying to pull a lot of data across a USB connection? There's also that stupid psuedo-swap process that the Pi uses (maybe gone now, don't know) that would tie a core or two up, maybe you're running out of memory and it's trying swap but can't?
I have had it happen in some cases.. Though, I am talking about a crazy mount of connections and nginx would probably not have those issues. I can't give more details because of reasons.
The Apache server that has the 100% CPU problem isn't on any of my PIs but on the Debian VM I rent from Lineode. I suspect the configuration may be too limited in memory. I don't really care because even when it runs at 100% CPU, the site still seem responsive enough. My cron job seems to take care of that problem though.
Yes, could definitely be memory related…or their VM are just poorly optimized and leaky.