Why I can't refit a tug into another? I thought that the only conditions were shipyard size (nature of SY, obv!) and that the ship would not be damaged, but aside that, even if the decision could be stupid (very huge cost) nothing prevented you from refitting any ship into another one?

A shipyard tooled for Class A can only refit (or build) a ship into class B if:

• The cost of new components for class B relative to class A, plus a premium of 20%, plus another premium which is the relative size difference between classes A and B, is less than 20% of the build cost of class A
• There is an additional requirement that the tonnage of class B is less than 20% difference from class A.

These requirements I think were new in C#, at least the second one which prevents silly cases like refitting fighters into battleships. Note that a shipyard tooled for class B can refit from ships of class A regardless of the cost, as long as the size requirement (within 20%) is met.

A common example would be refitting a survey ship from geo to grav sensors, using a shipyard tooled for the geosurvey class. If the survey ship costs, say, 750 BP, and has two survey sensors, then you cannot replace the 2x geo sensors with 2x grav sensors, because the cost of the sensors is 100 BP each and 200 BP x 1.20 (for the extra 20% premium) = 240 BP which is 32% of the survey ship cost, much more than 20%. On the other hand, if the shipyard is tooled for a variant with 1x geo, 1x grav sensor, then you can build or refit to either class because the cost of the NEW components is 100 BP for a single sensor in either case, so the refit cost is 120 BP or merely 16%. On the other-other hand, if the shipyard is tooled for the gravsurvey class then you can refit FROM the geosurvey class without a problem.

For tugs, usually it is not possible to do a refit to a new class in a shipyard tooled for the old class because tugs are almost entirely engines, so upgrading a tug usually means a complete swap of engines which is most of the build cost (refit cost may even exceed 100% of the old variant cost very easily). If you have a shipyard tooled for the new class, then you can refit from the old class without a problem.

Again, note that the examples assume the same or similar size between classes. If the old tug class is 45,000 tons and the new tug class is 90,000 tons, you cannot ever refit from A to B anyways.

You can refresh most windows by re-selecting your race from the dropdown in the top left. I do this particularly on the Commanders window quite a lot.

I do too. 
But a dedicated button is more evident.

Oh, so ...

Ordnance Transfer System: 40 MSP per Hour
Cost 20   Size 500 tons   Crew 20   HTK 1
Materials Required: Duranium  5    Boronide  15   

is for missiles only?

Yes.   

You can refresh most windows by re-selecting your race from the dropdown in the top left. I do this particularly on the Commanders window quite a lot.

What could explain that my MSP freighter only transfers to Earth MSP at a rate of 10 MSP per hour, and not 40 as per the component it has?

Only a cargo shuttle bay is required for transferring maintenance supplies. There is no other component to increase the rate.
And shuttle bays do not specify a transfer rate, because the base rate never changes:

Maintenance supplies are transferred at the rate of 10 per hour, multiplied by the number of cargo shuttle bays and the racial shuttle technology.