Judging from the question and the comments, I'll paraphrase your question as:
I'd like to encrypt a file, but part of my file has a predictable format. Will this make it easier to crack the encryption? Should I leave the structured parts out and encrypt only the minimum?
First off: that's not a silly question. Intuitively, you would think that knowing about the structure of the message would help you decrypt it, and this is true—to a certain point.
Luckily, this issue has long been anticipated by cryptography. 'Modern' encryption algorithms have a high branching factor: a small tweak in the input, a single changed bit, will create an unrecognisably different output. Because of this, knowing the structure of part of your file will not help me much, because any variation in content will lead to a very different result.
High branching factors are essential to strong encryption. Here is a brief example(1) of this in action:
> echo HELO1 | openssl aes-128-cbc -k meep -S 0
> echo HELO2 | openssl aes-128-cbc -k meep -S 0
openssl <algorithm> -k <passphrase> -S <salt>
HELO2 have a similar structure—they differ by only two bits—but produce a very different output. This makes it so that, if I start guessing for your encryption key, I will have no idea of how 'close' I am. Basically, unless I get an exact hit and guess your passphrase, I'm going to have a hard time decerning anything from your file.
Unless, of course, you give me information by leaving your headers exposed. Not only do I now know the file type, I also have access to the Huffman tree, which was built from, and hence contains information about, the message it encoded. I may be able to make an educated guess about the contents without ever trying to decrypt it.
HTTP is a structured protocol as well: each request starts with a 'method' (GET, POST, PUT...) and ends with
HTTP/1.X with X some number. Even more: each line that follows has a predictable structure, as well as some lines which could be accurately guessed (
Host:). That sounds like a lot of information for me to use.
Yet HTTPS encrypts the entire conversation, because not doing so would give me a lot more information. Heck, with all the headers, I might not even need to decrypt the payload: I can blackmail you with just the header data.