I have a BSC (Hons) in information systems and I can understand how hard it is to phrase or define certain systems, as technology is evolving at such a rapid pace. Aggregates in the context of this sentence suggests the plural and that there are many information systems involved. If there is more than one the plural form of technologies should be used.
Please allow me to say that the correct term for these systems would appear to be Transactional Processing Systems.
To rephrase your sentence:
(Company) develops transactional processing systems that aggregate payment information for service providers and merchants.
Computer Applications or Specialised software may also be used instead of technology / transactional processing systems if the intended audience is not from a technical background.
In your sentence, the correct option would be the second sentence as technology is singular. See here
To use the sentence without an 'a' in it just change technology to technologies so that it reads:
(Company) develops transactional data technologies that aggregate information for payment service providers and merchants.
Does this help?