Am I just being paranoid or are my concerns justified?
Here's a rough list of the mods listed as having dirty entries:
Spoiler
Fields of Kummu Expanded
Midnight Dragon's Earthly Delights mod (includes changes to the Acrobat class)
Assassin's Armoury
Nevena's Twin Lamps & Slave Hunters (LOTS of item & door entries)
Great House Dagoth
Adamantium Armour
Grow Your Own Telvanni Towers [final] (unclean doors)
LGNPC Ald-ruhn v1.3
LGNPC Seyda Neen (dialogue deleted)
Building Up Uvirith's Grave 1.1 (deleted items, this might just be to level the floors out as the creator previously suggested)
Crusader Class Fix
Ash Ghoul Hearts
Less Lore
Nerevarine Greeting Tweaks (dialogue deleted)
Her Tamed Lightning (dialogue deleted)
Lore Fix (dialogue deleted)
TransportMH (dialogue deleted)
Less Generic Bloodmoon (dialogue deleted)
Siege at Firemoth (unclean doors)
St Lothis Fix (unclean enchantment)
Warhammer fix (something to do with werewolf health)
Area Affect Arrows
Rank Advancement Revamped (companion entries, popups and werewolf values)
Mining Mod v1.5 Tribunal
Master Index
Better Moon and Star
Entertainers
EBQ Artifact
Sadrith Mora Docks
Dwemer Ruins Fix2
Clean Combat Angle Adjustment
Abot Guars v1.15
GOTY Script Tidy (Morrowind Patch Project version) (identical script to default entry)
Ghostgate shrine fix
Almalexia_voicev1
Brittlewind fix (brittlewind spell entry identical to default entry)
Weapon range balance (weapon entry identical to default entry)
Weapon Rotate - Tribunal (nerevarbladeflame entry identical to default entry)
Fields of Kummu Expanded
Midnight Dragon's Earthly Delights mod (includes changes to the Acrobat class)
Assassin's Armoury
Nevena's Twin Lamps & Slave Hunters (LOTS of item & door entries)
Great House Dagoth
Adamantium Armour
Grow Your Own Telvanni Towers [final] (unclean doors)
LGNPC Ald-ruhn v1.3
LGNPC Seyda Neen (dialogue deleted)
Building Up Uvirith's Grave 1.1 (deleted items, this might just be to level the floors out as the creator previously suggested)
Crusader Class Fix
Ash Ghoul Hearts
Less Lore
Nerevarine Greeting Tweaks (dialogue deleted)
Her Tamed Lightning (dialogue deleted)
Lore Fix (dialogue deleted)
TransportMH (dialogue deleted)
Less Generic Bloodmoon (dialogue deleted)
Siege at Firemoth (unclean doors)
St Lothis Fix (unclean enchantment)
Warhammer fix (something to do with werewolf health)
Area Affect Arrows
Rank Advancement Revamped (companion entries, popups and werewolf values)
Mining Mod v1.5 Tribunal
Master Index
Better Moon and Star
Entertainers
EBQ Artifact
Sadrith Mora Docks
Dwemer Ruins Fix2
Clean Combat Angle Adjustment
Abot Guars v1.15
GOTY Script Tidy (Morrowind Patch Project version) (identical script to default entry)
Ghostgate shrine fix
Almalexia_voicev1
Brittlewind fix (brittlewind spell entry identical to default entry)
Weapon range balance (weapon entry identical to default entry)
Weapon Rotate - Tribunal (nerevarbladeflame entry identical to default entry)
I can post the full list if that would help, but in its raw form it's too long to fit in a single post.