'bioinformatics' is a very general term which includes a wide range of different fields; therefore, it is very difficult to develop a single library to solve the needs of all bioinformaticians at once, and this is what the Bio* project fail to see now.
All the Bio* projects like BioPerl and BioPython are organized as a single module with a wide range of different functions, that you have to install as a block in order to use. For example, if you need to use the PhyloXML parser from BioPython, you need to install also the BioPython libraries to parse Fasta files, to query the NCBI databases, etc..
This is a very different situation compared to Bioconductor, where you have many independent libraries, including some redundant and some abandoned, but where you can install only the library you need, and where you can choose between different solutions to the same problem. From this point of view, I don't trust them when I think that they have not found a solution to this matter yet.
From another point of view, I like the Bio* projects because I recognize the effort they have done in making the bioinformatics community more compact. Thanks to BioPython, I learned that rather than developing my custom Fasta format parser I should use a library which is tested carefully before being released and that is being used by other people, making my results more comparable. From that, I am a great supporter of the Bio* projects.
Moreover, these projects are also a place to meet other programmer working in the same field and to discuss on the best implementation for each algorithm, which is something that would not be so easy without them.
In any case, regarding your question, my answer is: I will trust more your results if you use the Bio* libraries than if you develop the library by yourself. The Bio* libraries are tested very carefully before being released, and are used by many people in different environments and on different projects. Moreover, if an error is found in a Bio* library, then it will be easier to know which experiments have used the Bio* version with the bug and repeat the analysis with the correct implementation. So, if I were the reviewer of your paper, I will trust more the Bio* libraries than your custom implementation.