I don't see any problem. I have xx sites under my main website, connected both to GA and WMT. These are real clients and different individuals. I also have a number of personal sites under the main one (developed by/etc). Never had any issue.
I own around 30 websites under the same parent company. There's very little interlinking, but Google knows they're connected, because they're under the same GA account.
Although rare, I've had individual sites penalised, and I can confirm that it does not affect other sites. Could be a fluke, but whenever this has happened to a site, another in my portfolio tends to increase SERP rankings.