Generally speaking, the size of an .htaccess file could have a small effect on the server the first time it is processed after a change as the server incorporates new rules, but this effect should be minimal.

However, mod_rewrite does have inherent overhead resulting from the use of the rewrite engine. For massive 301 redirects, it might be less resource intensive to use RedirectMatch directives which work similar to mod_rewrite for 301 redirects. The main difference is that the rewrites are based solely on the original URL, and additional conditionals can not be added. However, it sounds like that is not a major factor in what you are trying to do. The directive is used as follows:

RedirectMatch permanent /oldfolder/(.*) http://www.yourdomain.tld/newfolder/$1
RedirectMatch 301 /(.*).html http://www.yourdomain.tld/$1.php

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