It was confirmed today that when you target your ad to more than one subreddit it will also show on the frontpage of Reddit when users who subscribe to one of your targets is logged in. Redditor SerialAlibi asked the question in the SelfServe advertising subreddit to make sure the ads would not appear on /r/all to irrelevant users. For example if your ad targeted the /r/NoMansSky, /r/diy, and /r/awww anyone subscribed to those subreddits would see your ad on the homepage.
Reddit Staffer MyNameIzKhan replied confirming that ads would indeed appear on the homepage.
Yes, your ad will be displayed to the frontpage of users who are subscribed to your targeted subreddits.
Many subreddits can have low pageviews and therefore be difficult to obtain advertising inventory on. Having your ads automatically appear to target users on the frontpage offers a new way to reach them helping avoid odd timing issues or situation where advertising inventory is almost never available.
This isn’t something you can turn off, so be aware that when targeting a subreddit your ad might also be on the home page of the site and may not reach active users in that precise subreddit you wanted to target. While this doesn’t allow for the granular level of targeting some advertisers might want, it does ensure better exposure of your ad to your target audience.