I'll see what I can tell you about your motor.
By the production number (serial) I make it as a built in late 1992 and probably sold as a new 93 model. BUT since the year of mfg is not encoded in the serial, it absolutely could have been sold as a "brand new" 1994 model if it sat around a couple years after it was built - I (personally believe) Merc did that on purpose so they wouldn't have "old stock/out of date models" sitting in the showroom.
I believe this model, and it's sister the 5 horse, were built by Tohatsu for Merc - they have a Japanese style carb and ignition system which Merc never used on their own designed/built models. This would be nothing new. For years Yamaha built major components and total motors (some Mariners) for Merc. After a falling out, Merc entered into a joint venture with Tohatsu and Tohatsu now builds most of the Merc 4 strokes under 40 horses in power.
Anyhow, there is no thermostat listed or shown in the parts lists/diagrams for this model as far as I can see. I don't have a service manual for this model as it was not included in the master set covering your possible model years (which reinforces to me at least that this was NOT a Merc built model, simply Merc "branded").
I'm not sure which "two holes" you are referring to from your description of where they are located. There is a strainer on the underside of the cavitation plate (so directly above the prop, but on the underside of the plate) where water is "sucked in" to water pump. Given that there does not appear to be a thermostat an inconsistent water flow from the tell-tale (may) indicate an issue somewhere in the system.
That could be anything from the impeller, to any of the gaskets/seals on the water pump cover - a compromised water tube, partial blockage somewhere in the tube itself or the water channels in the power head etc. If the bubble you note are coming from the pick-up tube strainer that would further reinforce that it's either not pumping correctly, or a seal somewhere is compromised and all the water is NOT being directed to the powerhead.