No penalty. A "penalty" is a serious specific action by Google applied to your site. The question is probably better asked 'does Google devalue your site in any way by what is sees as direct traffic.'

If you want valid traffic stats, don't use Google Analytics... use your server logs.

Good idea, since moving hosts i hadn't re-enabled custom metrics, going to pump my stuff to sumologic and see what it says. Either way, it is weird that so much of this direct traffic doesn't seem to convert/count for anything. I'll keep a close eye on this and report back. Mostly curious if others have seen similar quirks.

this direct traffic

Only by looking at your raw access logs can you tell whether this “direct traffic” even exists, or is simply a robot requesting your analytics file in isolation.

I don't know if there are solid statistics comparing trafic source with ad success. I do know that the sites for which I've disabled my own ad blocker are all sites that would come through as Direct Traffic: they're either bookmarked, or I type two or three letters and the browser knows what I mean.

It's traffic that isn't recognized by google analytics with a referring source (digging around to see if i can match it or fix it..), but i definitely see the increase in traffic and my WAF says its human.. not seeing bots/same ip/bad refers and garbage...

Well, does the burst in traffic show in the pageviews/adviews/clicks statistics of adsense?