How do I mark mail as read in Lotus Notes without actually opening the email?

Select your email messages and under Edit -> Unread Marks -> Mark Selected Read will do it.

Update

Pulled up comment from @Leons

Under Notes 8.5, you can make the behavior default in:

File > Preferences > Basic Notes Client Config

and check the box in the Additional Options list box:

[x] Mark documents read when opened in preview pane

You can also hit the insert key to toggle read status.

The best way is to go to Preferences > Basic Notes Client Configuration > Additional Options > Mark documents read when opened in preview pane.