Are basic replacement ciphers always bad for structured data encryption?
A good encryption should produce data that are indistinguishable from a random stream. If you simply replace bytes with other bytes, and each byte has always the same replacement, many statistical characteristics of the original message remain. For instance, if the original message is text, then the frequency of each letter will remain also after applying byte-by-byte replacement.

by encrypting the data with other methods before passing it through
the basic cipher

If you encrypt the data with other methods, for instance with AES, there is no need to do any further encryption of the encrypted message. AES is unbreakable.
The question about multiple encryption was answered on SE many times. See for instance this.