Если не считать сифона для грунта, все инструменты, включая сачок, чистые.

Yes, если is literally if, but the whole expression если не считать works as an idiomatic phrase meaning if you don’t count, leaving aside, or simply except for.

So:

• Если не считать сифона для грунта...
  = If you don’t count the gravel siphon...
  = Except for the gravel siphon...

A native English speaker should think of this as a set phrase, not as a real conditional in the normal if X, then Y sense.

Here сифона is in the genitive singular.

That happens because after a negated verb, Russian often uses the genitive instead of the accusative, especially in set expressions like если не считать. So если не считать сифона is a very natural way to say if we don’t count the siphon / except for the siphon.

For a learner, the safest takeaway is:

• если не считать + genitive is a very common pattern

So in this sentence:

• сифон = dictionary form
• сифона = genitive singular used after не считать

Для means for, and it requires the genitive case.

So:

• грунт = gravel, substrate, soil, ground
• для грунта = for gravel / for the substrate

In aquarium contexts, грунт usually means the material at the bottom of the tank, such as gravel or substrate.

So сифон для грунта is literally a siphon for the substrate/gravel, i.e. a gravel siphon.

Включая means including, and it normally takes the accusative case.

So:

• сачок = net
• включая сачок = including the net

Since сачок is an inanimate masculine noun, its accusative singular looks exactly like the nominative singular:

• nominative: сачок
• accusative: сачок

That is why the form does not change here.

Because включая сачок is an inserted clarifying phrase: including the net.

The main structure is:

• все инструменты ... чистые
  = all the tools are clean

And включая сачок is extra information added in the middle:

• all the tools, including the net, are clean

The first comma, after Если не считать сифона для грунта, is there because that whole opening phrase functions like an introductory expression: Except for the gravel siphon, ...

Because the subject is plural:

• все инструменты = all the tools

So the predicate adjective must also be plural:

• чистые = clean (plural)

Grammatically:

• все инструменты = nominative plural
• чистые = plural form agreeing with инструменты

So the core sentence is:

• Все инструменты чистые.
  = All the tools are clean.

Russian has both long-form and short-form adjectives.

Here:

• чистые = long form
• чисты = short form

Both can be used predicatively, but they do not sound exactly the same.

In modern everyday Russian, the long form чистые is extremely common and neutral in sentences like this:

• Инструменты чистые. = normal, natural

The short form чисты is possible, but it sounds more formal, literary, or stylistically marked.

So чистые is the most natural everyday choice here.

Yes. All of these can work, but they have slightly different shades of style.

• Кроме сифона для грунта, все инструменты, включая сачок, чистые.
  = Except for the gravel siphon, all the tools, including the net, are clean.

• Не считая сифона для грунта, все инструменты, включая сачок, чистые.
  = Not counting the gravel siphon, all the tools, including the net, are clean.

• Если не считать сифона для грунта...
  sounds a little more like if we leave aside / if we don’t count

So:

• кроме = simplest, most direct except for
• не считая = compact not counting
• если не считать = slightly softer or more parenthetical

In normal usage, yes, that is the natural implication.

If you say:

• Если не считать сифона для грунта, все инструменты... чистые

you are basically separating the siphon from the group of clean tools. That strongly suggests the siphon is not clean.

Strictly speaking, the sentence frames it as an exception rather than directly saying the siphon is dirty, but that is clearly the intended meaning in most contexts.

Russian word order is fairly flexible, so the sentence could be rearranged. For example:

• Все инструменты, включая сачок, чистые, если не считать сифона для грунта.

This would still be understandable. But the original order is natural because it puts the exception first:

• Если не считать сифона для грунта, ...

That sets up the listener to interpret the rest of the sentence as a general statement with one item excluded.

So the original word order is good because it highlights the exception right away.