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does Linux block ports and interrupts for user programs use ?

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The only interrupt a non-kernel program should be using is int 0x80, which is the interrupt to request one of the system calls listed in /usr/include/sys/syscall.h. If you want to directly interact with hardware interrupts, this should be done inside a kernel module. A good introduction to Assembly on a Linux system. This thread should also be useful for you.

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As noted in the LinuxQuestions thread I linked to, a program like dosbox.com or dosemu.org will do the same interrupt emulation that windows provides for assembly programs (even with windows you are not really using interrupts, but getting pseudo-interrupts though an emulator). – Justin Smith Feb 21 '10 at 15:41
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