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Has your house ever been hit by lightning before?
If lightning is common in your neighborhood, I'd say the best defense is to have a dedicated lightning rod somewhere else on your property (some distance away from your antennas) that extends higher than your TV mast.
Surge protection and grounding of your TV antenna will protect your equipment from *indirect* lightning strikes, but if you ever get a direct hit, chances are that your equipment will not survive no matter what.
Consumer-grade surge suppression equipment might save you from mild spikes (e.g., power grid switching on after a blackout, indirect lightning strikes on power/cable/telephone lines, etc.), but nothing as intense as a direct strike on your house.
In regards to your more general question about signal loss along the coax... Yes, it's possible to have some extra signal loss caused by a junction point in the cable. The amount of loss will depend a lot on how bad the impedance mismatch is at the junction. The loss from splicing two sections of identical coax together is usually insignificant if the connectors and components are built well (~ only a fraction of a dB).
Splitters, directional couplers, baluns, filters, and other frequency-sensitive components are more likely to have impedance mismatches that will cause some signal to be reflected back the way it came. There may also be internal inefficiencies that cause some signal to be lost as well.
The coax itself is also responsible for signal loss over distance.
If your signals are weak to begin with, and you are concerned about every bit of signal loss along the way because you want to preserve as much signal quality as possible, then what you really need is a good pre-amp installed close to the antenna (which I think you already have).
If you have a pre-amp installed, most of the losses downstream from the amp become insignificant and, for the most part, can be ignored. You just need to make sure the gain in the amp is sufficient to overcome the downstream losses that you incur. To maintain the best possible SNR, you'll want your pre-amp to have a low Noise Figure rating.
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