I would be interested if you book for any niche site an extra webspace package or IP or they build it on existing webspace. Furthermore, if you ever choose a new template for your niche sites. I had this problem, I have constructed about 10 niche sites with a similar template and on the same IP, content or the themes were completely differently. The projects were all well maintained with WMT accounts. After almost 2 months I received a manual penalty with respect Thin content for all 10 projects. Do you have this experience? Looking forward to reply.
Your question touches on two topics that are not directly related.
Firstly, the question of whether I have all the niche site on a web space or not. This is not at all the case, as I have different tariffs and server hosting my sites and there a little distribute. But not for SEO reasons, but not to all sites and blogs in the failure of a hoster.
For SEO reasons, I believe such an approach to be not necessary, even if others swear by it. But the only safe thing is that they do not go on good content, but use SEO tricks.
Since we are already talking about the second topic, your penalty because of “thin content”. I assume that the penalty was not directly what to do with the fact that you had all the sites on one hosting account. Instead, Google will already have reasons to call your Content as “thin”. Apparently all 10 niche sites were not particularly high and perhaps linked with each other.
It may be that the fact that all were on a web space, Google has in its assessment reinforced, but the main reason it was not safe. I sometimes use different niche sites on a webspace and I have no trouble with Google.
Before you choose to blame IPs and web spaces, you should critically analyze whether Google with accusations of “thin content” is right and what you should do differently in the future.