Thing is, total mana lost is equivalent to mana deprivation on a turn by turn basis because mana can be stockpiled.
To illustrate this, consider the total mana of a 10 channelling wizard (A) vs. a 10 channeling wizard (B) over the course of 12 turns, assuming they start at 10 mana before turn 1 (and so immediately channel). On turn 1, A will cast a Mana siphon:
A:
(20) -> (Casts Mana Siphon: -12 Mana) -> ( 8 )
(18)
(28)
(38)
(48)
(58)
(68)
(78)
(88)
(98)
(108)
(118)
B:
(20) -> (Hit with Mana Siphon: -2 channeling)
(28)
(36)
(44)
(52)
(60)
(68)
(76)
(84)
(92)
(100)
(108)
As you can see, by round 7 Wizard A has caught up to Wizard B, and thereafter has a mana advantage. Now Suppose Wizard A casts 2 walls (we'll assume he uses 2 different actions to do this, to save mana, and uses walls costing 5 mana each):
A:
(20) -> (Casts Mana Siphon + Wall: -17 Mana) -> ( 3 )
(13) -> (Casts Wall: -5 Mana) -> ( 8 )
(18)
(28)
(38)
(48)
(58)
(68)
(78)
(88)
(98)
(108)
Here, the wizard has not caught up until the 12th round; up until that point, the drained wizard has more mana.
In what circumstances would having less mana on a per-turn basis be a disadvantage in of itself? The only one I can think if is if your opponent is going for a mana deprivation strategy, complete with power drain, in which case you cannot stockpile mana. Of course, the correct response in that case is to spend all of your mana every turn as quickly as possible until you find a way to protect yourself against the mana deprivation, so I don't think it inconveniences you much even then.
Now, if there is a place you want to put a wall and you decide to put a mana siphon there, all well and good. But placing a wall for the sole purpose of protecting the mana siphon is a waste of mana.
Think of a mana siphon like a mana flower/crystal - you would never use a wall to protect one of those, right? (the mana siphon takes 1 more turn to pay off, but gives you a relative advantage of 2 more mana per turn, so it is like a better version of the mana flower/crystal)
Also, being incorporeal, siphons are relatively sturdy. It would take a concerted effort (or a couple quickcast Arcane Zaps...) to take one out, which would give you a tempo advantage. Why discourage your opponent from attacking it?
Personally, I never use mana siphons. Essence Drain on an important creature is much cheaper (pays off in 3 turns) and has more or less the same effect.