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There are a number of issues with your existing example:
1. Your <<if>> and <<else>> macro calles are malformed, the set calls should be within the macro's body.
<<if $topless is 1 and $bottomless is 1>>
<<set $naked to 1>>
<<else>>
<<set $breezy to 1>>
<</if>>
2. You apear to be using numbers to indicate a Boolean state.
If a variable can only be one of two possible values (yes/no, on/off, true/false, ect..) then it is considered a Boolean data type, which means you should be using the true and false literal values instead.
<<set $topless to false>>
or
<<set $topless to true>>
... and your <<if>> macro would then look like the following.
<<if $topless and $bottomless>>
<<set $naked to true>>
<<else>>
<<set $breezy to true>>
<</if>>
NOTE: You should initial all your story variables before you use them, and the ideal place to do this is within your project's StoryInit special passage.
<<set $topless to false>>
<<set $pantsless to false>>
<<set $bottomless to false>>
<<set $naked to false>>
<<set $breezy to false>>
If you were using <<link>> macros then I would suggest replacing the ones in your example with <<linkreplace>> macros, but you are using the <<button>> macro and there isn't a 'replace' variation of that so you will need to do it the long way.
EDIT: Added two extra examples: one using Boolean variables; and one using Booleans and the <<remove>> macro.
The following uses Custom Style markup to define three IDed areas on the page, and then uses the <<replace>> macro to clear out each of these areas as needed.
@@#remove-shirt;<<nobr>>
<<button "remove shirt">>
<<set $topless to 1>>
<<replace "#remove-shirt">><</replace>>
<</button>>
<</nobr>>@@
@@#remove-pants;<<nobr>>
<<button "remove pants">>
<<set $pantsless to 1>>
<<replace "#remove-pants">><</replace>>
<</button>>
<</nobr>>@@
@@#remove-underwear;<<nobr>>
<<button "remove underwear">>
<<if $topless is 1 and $bottomless is 1>>
<<set $naked to 1>>
<<else>>
<<set $breezy to 1>>
<</if>>
<<replace "#remove-underwear">><</replace>>
<</button>>
<</nobr>>@@
The following example is the same as above except it uses Boolean based variables instead of Number based variables.
@@#remove-shirt;<<nobr>>
<<button "remove shirt">>
<<set $topless to true>>
<<replace "#remove-shirt">><</replace>>
<</button>>
<</nobr>>@@
@@#remove-pants;<<nobr>>
<<button "remove pants">>
<<set $pantsless to true>>
<<replace "#remove-pants">><</replace>>
<</button>>
<</nobr>>@@
@@#remove-underwear;<<nobr>>
<<button "remove underwear">>
<<if $topless and $bottomless>>
<<set $naked to true>>
<<else>>
<<set $breezy to true>>
<</if>>
<<replace "#remove-underwear">><</replace>>
<</button>>
<</nobr>>@@
The following example is the same as above except it uses the <<remove>> macro instead of the <<replace>> macro.
@@#remove-shirt;<<nobr>>
<<button "remove shirt">>
<<set $topless to true>>
<<remove "#remove-shirt">>
<</button>>
<</nobr>>@@
@@#remove-pants;<<nobr>>
<<button "remove pants">>
<<set $pantsless to true>>
<<remove "#remove-pants">>
<</button>>
<</nobr>>@@
@@#remove-underwear;<<nobr>>
<<button "remove underwear">>
<<if $topless and $bottomless>>
<<set $naked to true>>
<<else>>
<<set $breezy to true>>
<</if>>
<<remove "#remove-underwear">>
<</button>>
<</nobr>>@@