I'm looking to go somewhere over the Easter Break (06/04/12 -09/04/12) where I won't be affected by shops, attractions and services such as trains closing, will I be affected by such things in Bosnia over this period?
According to Wikipedia the largest religious group is Islam (40%).
Depending on where you plan to stay in Bosnia, you'll meet predominantly Christians or Muslims.
Easter and Easter Monday are public holidays there so larger cities like Sarajevo or Banja Luka will have shops and monuments closed. Most of the bars, cafes and restaurants will be open and perhaps some smaller shops.
But if you decide to you stay at smaller towns or rural areas where there's mostly Islam followers such as Travnik, Tuzla or Zenica, I believe you won't have any trouble finding an opened establishment of any type. Of course, there will still be some places that are closed not because of the Easter or the day after but because people just like to take the day off.
In Bosnia (and Herzegovina), the government does something slightly differently, due to the diversity of religion. In addition to certain public holidays (including Easter), each person is permitted two working days per year to fulfill their religious needs. These days are not considered official public holidays, but if taken around other public holidays (Easter, Christmas, Orthodox Christmas) could mean a lot of people are away / their shops are closed then.
Note that Good Friday and Easter Monday are public holidays according to some sites.
As far as trains go, there's no mention on the booking site for trains of holidays or Easter. The online booking can only be done a month in advance, so can't check that. However, you could email them on info@zfbh.ba and ask.
The Julian calendar Easter (celebrated by Orthodox Christians, ie. Serbs in Bosnia) is April 15th, so at least in the Serbian parts of Bosnia, it will be "business as usual" the weekend before Easter (when you want to visit).
