Not an expert on this issue, but I found this:
Between NTFS and FAT32, If you use the drive only in Windows, use NTFS. In any other case, use FAT32.
Why NTFS for Windows?
NTFS(New Technology File System) was introduced by windows and has been supported since the early versions of Windows. So it has become sort of a Windows thing.
Is the native file system for WinNT/2k/XP
Allows indexing which improves file searching (mostly, faster); causes slight performance hit (can turn off).
Has better security -- such as file-wise encryption (not supported by WinXP home) and per-user access rules (you can stop your wife from seeing the porn folder!)
Supports user quotas (prevent the tykes from downloading too many mp3s)
Has file-wise compression.
Is journaled, decreasing data loss (ScanDisk at start up unnecessary).
Uses Unicode (allows foreign and extended character) file names and natively supports long file names.
Supports larger files than FAT (greater than 4GB).
Allows larger volume sizes (greater than 1TB) There is talk about a theoretical limit of 16 Exabytes, and up to 2 Terabytes.
Supported format on dynamic disks (no dynamic disks on WinXP Home).
Works well with large cache (greater than 96MB systems).
Performs better on volumes ~20GB and more.
Is more space-efficient on large volumes (greater than 8GB).
Resistant to fragmentation.
If this is correct, and you only use your SDcards or USB drives etc with Windows, there is no problem with NTFS. However, my brain is sufficiently shrunken so that I stand corrected by any larger brains on the forum!