If I opt for the five minute connection and miss the train, I assume I
can catch the one a half hour later.
Yes. You can take any train that day on that route.
If I reserve a seat, I would just lose that portion of the ticket,
right?
Correct. CHF 5.00
The train I was looking at was an 11:30 train with only one connection
in Interlaken Ost.
I wonder what you mean. 11:30 leaving from which station? Trains from Interlaken Ost going in this direction leave at :29 and :59 each hour.
Follow Travelergirl’s advice - get ready and be at the door before you arrive in Interlaken Ost. You will exit this train on the right hand side. If I am in a hurry I usually look out the window as we arrive at the train station to see when we pass the stairs or ramp down so that I know which way to start walking once I exit the train.
I have had the train from Lauterbrunnen arrive in Interlaken Ost a few minutes late. It has happened a few times and each time they made an announcement on the train that the train toward Bern (the one you want to catch) would wait for a few minutes longer.
Lots and lots of people try to make this connection. You will not be the only one.
We will have luggage with us so I thought a reservation would make
that easier?
At only 5.00 per seat, you can certainly just get them if you want to. In the overall expense of your vacation, this is certainly nothing. You will then have to find that exact carriage on the train, easier to do from the outside (I reserve seats all the time in Germany, but never in Switzerland). If you are running late just jump on the train as soon as you can, then worry about finding your exact seats.