Just because you can’t observe the microscopic event doesn’t mean you can discount the macroscopic effects. When you burn natural gas, water is produced; you don’t need to see the constituent molecules reacting in order to see that water forms and, against all safe lab practice, taste it to confirm its water.
The bonding of water can also be observed in the macro-scale, in the form of snowflakes. Each snowflake has six-sided (or six-fold?) symmetry because of the way that water bonds and freezes.
There are ways of imaging molecules. It does require some advanced techniques and you do not get images like you may be used to but they rather have to be interpreted. Other then that chemistry is very practical as you can see how diferent chemicals interact. It is not that different then other branches of science.
We’ve been able to image electrons around nuclei since 2011: https://gizmodo.com/fascinating-first-ever-images-of-an-electron-in-orbit-5835164
We’ve had images of bonds being broken and reformed since 2013: https://www.extremetech.com/extreme/157048-the-first-ever-images-of-a-molecule-as-it-makes-and-breaks-atomic-bonds
But we knew all this beforehand anyway from careful observation and experimentation.
In a sense, yes. Even the most complex and accurate descriptions science has of how things work on the atomic level are just models that fit all of our observations and measurements.
That’s all science is, really. Somebody says “hey, I wonder if it is this way?” and then tries to gather evidence for that hypothesis
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