I thought you could assign a value to the hash like

$vHash{"101010"}{"S0"} = "sometext";
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and then go on and assign an level of hash

$vHash{"101010USED"}{"S0"}{"SYSTEM"} = "sometext";
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You can, but you probably shouldn't. The first example puts sometext (which you needn't double-quote, since you aren't interpolating) into the key SO (which you needn't quote at all, since hash keys auto-quote) of the anonymous hash that lives at key 101010 of %vhash. That is, this is the same as

${ $vHash{101010} }{S0} = 'sometext';
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The second assignment treats $vHash{101010}{S0} $vHash{101010USED}{S0} as a hash by looking for its entry at key SYSTEM, so Perl obligingly makes it a hash. That is,

ref $vHash{101010}; # => 'HASH'
ref $vHash{101010}{S0}; # => undef
ref $vHash{101010USED}; # => 'HASH'
ref $vHash{101010USED}{S0}; # => 'HASH'
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While there's no need for the entries of a hash to be homogeneous—it's perfectly OK if some entries are hashes, some are hashes-of-hashes, and so on—it'll probably lead to confusion unless you really mean it.

UPDATE: As ikegami points out, one of the ways that it can confuse is that you can wind up treating a simple scalar as a (symbolic) hash reference, with the sort of unexpected results that you've discovered.