If you get a warning from Perl that you don't understand then it's always worth checking the full description in perldiag. In this case, it says:

Using a hash as a reference is deprecated
(D deprecated) You tried to use a hash as a reference, as in %foo->{"bar"} or %$ref->{"hello"} . Versions of perl <= 5.6.1 used to allow this syntax, but shouldn't have. It is now deprecated, and will be removed in a future version.

I assume that the fact it used to work has something to do with the internal representation of hashes (and also arrays) as something similar works in C.

But as the warning says, this usage is deprecated. And if something is deprecated, you shouldn't use it.

p.s. It's a "question", not a "doubt".

I know that it is deprecated, I never used this %hash->{key}, I came across some code like that, wanted to understand how it works; for my knowledge.
my question is, I can understand what is going on when I do $hash{key}, but I can't understand what is going when I do %hash->{key}, kindly explain.

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Vivek
-- 'I' am not the body, 'I' am the 'soul', which has no beginning or no end, no attachment or no aversion, nothing to attain or lose.

What is going on is that Perl is exposing more of its internals than it really should be. The name of the hash is being interpreted like a reference when you use this syntax.

%hash->{key} should never have worked, but some people noticed that it did and (wrongly) started to use it. And that's why it's just deprecated and hasn't been removed from the language yet.

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but I can't understand what is going when I do %hash->{key}, kindly explain

There is nothing to understand or explain, other than that %hash->{key} should have triggered a syntax error in Perl. Some older Perls didn't and therefore this error was downgraded to a warning to avoid breaking existing scripts.

A reference should always be a scalar (which can be part of an array, a hash or indeed an object or the return value of a subroutine, but not the array, hash, ... itself.

BTW you will trigger a similar warning with the following:

@array = qw /1 2 3 4 5/;
print @array->[1];
[download]

It really is the same issue.

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James