There are multiple reasons that this could happen. But in your case, I think it is due to the reason below.
Marketo embeds a 1X1 invisible image in the email. Marketo will count that email as opened only if the lead enables download image in their email client. In most cases, an email client such as Gmail defaults it to not open. However, when a lead clicks on the link, Marketo will also infer that the email is opened since most likely the lead will have to open the email in order to click on the link. Note that this logic only applies to the report and in this case, both the Opened and Clicked Metric wil be incrememented by 1.
Smart List filters out leads based on the Activity Log. In the case where a lead click on a link but didn't open the email (i.e. download the invisible image), it will log the click link activity but not the open email activity. So that's probably why you are seeing less leads in your smart list. You can verify that information in the Lead Activity.
Here is an article that explain things further -
http://community.marketo.com/MarketoArticle?id=kA050000000KypPCAS