I have a new Tohatsu 5hp motor. I have decided to keep it on the transom after checking with the marine mechanic that it wouldn't hurt my 14' tinny transom. He suggested I install bolts through the motor/transom for security. Once I received the motor, i noticed I do not have any place available to do this.
I assume it will be okay after checking that my clamps are snugged down. The motor weighs 58lbs.
Thoughts?

Look again. If there is room for clamps, there should be some way to through-bolt. Even when tight, a small outboard can twist off of a transom under some conditions including sharp turns. I know, years ago I lost a small outboard off an inflatable dingy.

Use LOCK NUTS do not use lock washers

I disagree. I have had nylon lock nuts work loose from vibration many times. Plus, if they ever work loose, they need to be replaced because the nylon loses its gripping strength with repeated tightenings.
Use stainless flat washers, lock washers, and nuts. Once installed, you can cut/grind the ends of the bolts flush to the nut and use a pin punch to put a dimple between the nut and the screw threads. This will insure it doesn't loosen on it's own and you can still break it loose manually if you ever need to.

washer and lock washer?

yes, both, might even consider double nuts on each bolt as a locker

ps, if you would like some help, bring it and we can get that measured, centered, drilled and mounted