How to understand the meaning of ‘down a drain’？

Question

On his way to the sweet shop, he dropped his fifty pence and it bounced along the pavement and then disappeared down a drain.

1. Can I delete down a drain, and what is the difference between them？
2. Can I use in a drain to replace the down a drain？

Answer 1

"down a drain" is both literally here, i.e. the coin disappeared into the sewers, and figuratively:

If you say that something is going down the drain, you mean that it is being destroyed or wasted.

(source: Collins)

Note that the idiomatic use is with the definite article 'the', but English speakers will definitely be reminded of it with the indefinite article 'a'. That's probably the way it is worded, and not the other variations you suggest, which are grammatically fine.

Answer 2

On his way to the sweet shop, he dropped his fifty pence and it bounced along the pavement and then disappeared down a drain.

1. Can I delete down a drain, and what is the difference between them？
2. Can I use in a drain to replace the down a drain？

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A.1

On his way to the sweet shop, he dropped his fifty pence and it bounced along the pavement and then disappeared down a drain

meaning whilst on the way to the sweet shop, he lost his fifty pence down a drain

On his way to the sweet shop, he dropped his fifty pence and it bounced along the pavement and then disappeared

meaning whilst on the way to the sweet shop, he lost his fifty pence after dropping it

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A2.

Can I use in a drain to replace the down a drain？

yes

"On his way to the sweet shop, he dropped his fifty pence and it bounced along the pavement and then disappeared in a drain"

The meaning is slightly different, but not of any real relevance in regard to the meaning that your intended.