It's more a consequence of the bad design and implementation of the DER parser in OpenSSL, which is what most people use.
ASN.1 isn't actually a message format--it's the syntax for feeding to an ASN.1 parser generator, similar to protobufs.[1] There are multiple binary formats (BER, OER, PER, XER), but for X.509-based specs the binary format is DER. OpenSSL doesn't have a parser generator; just generic, low-level routines for slicing DER blobs.
If you used something like asn1c, you can simply feed it the X.509 ASN.1 specification and it generates a C-based parser and composer. Manipulating an X.509 certificate largely just becomes a matter of manipulating strongly typed C data structures.
For a recent Lua project I implemented an X.509 certificate parser using LPeg. Because PEGs are so expressive and I only cared about DER, it was much easier to skip dealing with ASN.1. DER is a TLV encoding, which isn't context free and thus not strictly compatible with PEGs, but LPeg has some extensions--e.g. match-time captures (http://www.inf.puc-rio.br/~roberto/lpeg/#matchtime)--which make it possible to create grammars for TLV encodings. Which, incidentally, is one reason not to use length-prefixed encodings: they're not a context-free grammar, which makes it more difficult and sometimes impossible to use a parser generator; length prefixing is a mitigation for a specific class of bugs that are common when open-coding a parser, but parsers for complex formats (i.e. many typed, compound objects with deep nesting) shouldn't be open-coded if you can help it.
[1] Except ASN.1 is better designed--it lacks all the ambiguous cases. See http://lionet.info/asn1c/blog/2010/07/18/thrift-semantics/
The downside to ASN.1 is that, especially at the time OpenSSL was originally written, documentation was expensive, and because the open source ecosystem typically used line-based protocols which can more easily be implemented with open-coded parsers, it's not surprising developers made some poor choices in the first open source X.509 certificate parser; choices which have haunted OpenSSL and open source projects more generally ever since.
