"Yes" to both questions. It is both in your head and there is a meaning behind them.

When a person sees a certain number and wonders about it's meaning, there's some mystery associated with it. Where there's a mystery, there tends to be a compulsion to solve it. When there's a compulsion to solve it, the mystery tends to stay in mind, perhaps subconsciously, and the person tends to notice related things more often than would normally be expected.

The meaning of any number can be determined with numerology. Actually, it's the vibration the number represents that can be determined.

The number 911 is psychic and spiritual and concerned with the welfare of the world. Similarly with 11:09, except 11:09 is more inclined to do things about it and less inclined to just exist within a concern.

What it means to you personally, if anything, will need to be determined by you. The "seeing the same number" articles may help.

Once you've determined whether or not it holds any special meaning for you and, if yes, what that meaning is, you'll be able to notice 911 and 11:09 without wondering what it means. It should then bother you a lot less or not at all.