It does not change anything during install, and you should use 64 bit.

Why 64 bit not 32?

1. I am using an x64 version of ubuntu because my server has more than 4GB of RAM.
2. 64 is bigger than 32 :)

ubuntu help says:

Which is Better - 32 or 64 Bits?

If you are doing heavy work where you have started to hit the 4GB memory barrier, then 64-bit is for you. Certain intensive tasks such as encoding video or audio also run significantly faster on 64-bit operating systems (NOTE: this is implementation specific).

Phoronix has done some testing (2009), comparing 32bit/PAE/64bit, and this seems to indicate that 64bit performs better than 32bit in almost all cases.

Early 64-bit adopters were plagued by incompatibility problems (most noticeably Java and Flash), however most issues have now been resolved.

Some applications such as Flash do run slower in 64-bit mode, however work continues to improve on this.

Other platforms which also come in 32 and 64-bit flavours may experience more problems especially due to a lack of 64-bit device drivers as incompatible user application. As Ubuntu is entirely open source, this is not the case as all hardware supported by Ubuntu works equally well in 32-bit and 64-bit environments. The same applies to open source user applications as well.

Which Should I Choose?

Unless you have specific reasons to choose 32-bit, we recommend 64-bit to utilise the full capacity of your hardware.

https://help.ubuntu.com/community/32bit_and_64bit

I can not really answer that question myself due to lack of knowledge, but I was wondering myself about that when I saw your post. This quite recent installation howto at least seems to point in the 64-bit direction (because the auther uses an ubuntu 12.04 x64 Server LTS in the tutorial.

Would be still great whether somebody who actually knows stuff could add some thoughts about the pros and cons 32 vs 64 bit here to enlighten us all though.