Yes "they" is correct when referring to inanimate objects. From Merriam-Webster:
those ones — used as third person pronoun serving as the plural of he, she, or it...
Your second sentence is incorrect because you are referring to multiple apples.
These are both correct.
Wash an apple and put it into a vase.
Wash some apples and put them into a vase.
The phrases
the same size
and
the same sizes
both have the right to exist, and are used to mean different characteristics of the objects which they describe.
If a class of objects can be dimensioned in two or more of ways, for example, pipe segments have the outer (or inner) diameter, wall thickness and the length, then, comparing two pipe segments, you can say
Those two segments have the same sizes.
if you mean that all dimensions of the two objects measure equal to each other (within some tolerance).
If in some context only specific dimension (like length, for instance) is deemed important, and other dimensions can be ignored, you can say about two pipe segments of two diameters
Those two segments have the same size.
if their length is what's currently important.
When talking of items of clothing, you can say of different pairs of shoes that they all have the same size, although no dimension of those complex shapes is the same if carefully measured: the shoe "size" is a marking, classifier, which is only approximately associated with a certain dimension.
Back to your example...
A filled sphere (a ball) has essentially only one dimension - the diameter. Often enough it is a hollow sphere, and the wall thickness can be taken as the other dimension, but if it is a solid sphere, there is no other dimension. This way when you only compare one dimension, it is more natural to use singular. But it would not be wrong to say
The diameters of those balls are [all] the same.
They have the same diameters.
Phrase "the same" when describing a dimension means "of the same value".
Best Answer
'It' is the farm. Although it contains the ploughland, the hayfield, the orchard, the pool, and the spinney, it is still one farm. It is considered as a whole.
You could replace 'it was' with 'they were', but you would lose Orwell/Blair's emphasis on the farm as a whole. He was a careful writer, and wrote deliberately. Orwell uses a farm to make an analogy with the Soviet state. In 1917 the Bolshevik revolution was deemed to have given the people (= the animals) control of the whole state (= the farm), as specifically one entity. It would be confusing and unfocused to say the people had control of Russia's rivers, mountains, forests, lakes, etc.