Gdtyjr

I have a Problem with coloring a cell in a table because it removes the upper line of the cell. I already found out that there are some issues with cellcolor and cline but I couldn't come up with a solution that works with multicolumn.

documentclassarticle
usepackageamsmath
usepackagemultirow
usepackagemulticol
usepackagerotating 
usepackage[table]xcolor 
usepackagesiunitx 

begindocument
 begintabularc
 cline3-6
 multicolumn2 & multicolumn4Anzahl der Nullstellen \
 cline3-6
 multicolumn2 & 0 & 1 & 2 & 3 \
 hline
 multirow18*rotatebox[origin=c]90Anzahl der Polstellen & 1 & $beginmatrix SI99.9percent \ SI37.7percent \ SI43.8percent \ SI45.1percentendmatrix$ & $beginmatrix SI99.9percent \ SI41.5percent \ SI67.5percent \ SI72.6percentendmatrix$ & multicolumn2 \
 cline2-5
 & 2 & $beginmatrix SI99.9percent \ SI72percent \ SI78.4percent \ SI77.8percentendmatrix$ & $beginmatrix SI99.9percent \ SI72.6percent \ SI92.5percent \ SI94.4percentendmatrix$ & $beginmatrix SI99.5percent \ SI72.7percent \ SI97.2percent \ SI98.3percentendmatrix$ & \
 cline2-6
 & 3 & $beginmatrix SI98.6percent \ SI-42.7percent \ SI95.7percent \ SI94.2percentendmatrix$ & cellcolorblack!25 $beginmatrix SI99.9percent \ SI73.4percent \ SI99.1percent \ SI99.3percentendmatrix$ & $beginmatrix SI99.9percent \ SI-40.1percent \ SI99.3percent \ SI96.7percentendmatrix$ & $beginmatrix SI99.7percent \ SI72.8percent \ SI99.4percent \ SI98percentendmatrix$ \
 cline2-6
 & 4 & $beginmatrix SI0percent \ SI67.8percent \ SI93.2percent \ SI93percentendmatrix$ & $beginmatrix SI99.5percent \ SI-23.5percent \ SI95.4percent \ SI93percentendmatrix$ & $beginmatrix SI99.9percent \ SI73.9percent \ SI5.3percent \ SI93percentendmatrix$ & $beginmatrix SI99.9percent \ SI74percent \ SI-87.1percent \ SI96.5percentendmatrix$ \
 cline2-6
 & 5 & $beginmatrix SI-99.7percent \ SI-82.9percent \ SI-99.4percent \ SI93percentendmatrix$ & $beginmatrix SI-99.8percent \ SI64.9percent \ SI2.7percent \ SI93percentendmatrix$ & $beginmatrix SI-100.5percent \ SI-69.8percent \ SI59.1percent \ SI93percentendmatrix$ & $beginmatrix SI-0.4percent \ SI73.9percent \ SI14.4percent \ SI93.1percentendmatrix$ \
 hline
 endtabular
enddocument

Btw can somebody tell me why I had to put 18 in multirow?

As @leandris has kindly suggested in a comment, to make sure that the horizontal line shows up fully, it suffices to (a) load the hhline package and (b) replace the cline3-6 directive in question with hhline~~----.

In addition, you may want to simplify your code considerably. For instance, by employing an array environment instead of a tabular environment, you can get rid of all $ symbols. There's no real discernible need for encasing the percentage numbers in SI...... wrappers.

(The "missing" vertical line to the left of the shaded cell is an artifact of the low resolution of the screenshot; in a normal pdf file it'll show up just fine.)

documentclassarticle
usepackagemathtools,hhline
usepackagemultirow
usepackagerotating 
usepackage[table]xcolor 
usepackagesiunitx 

begindocument
[
setlengthextrarowheight1pt
beginarray*6
cline3-6
multicolumn2 
& multicolumn4textAnzahl der Nullstellen \
cline3-6
multicolumn2 & 0 & 1 & 2 & 3 \
hline
multirow17*rotatebox[origin=c]90Anzahl der Polstellen 
& 1 
& beginmatrix*[r] phantom-99.9% \ 37.7% \ 43.8% \ 45.1%endmatrix* 
& beginmatrix*[r] phantom-99.9% \ 41.5% \ 67.5% \ 72.6%endmatrix* 
& multicolumn2 \
cline2-5 
& 2 
& beginmatrix*[r] phantom-99.9% \ 72.0% \ 78.4% \ 77.8%endmatrix* 
& beginmatrix*[r] phantom-99.9% \ 72.6% \ 92.5% \ 94.4%endmatrix* 
& beginmatrix*[r] phantom-199.5% \ 72.7% \ 97.2% \ 98.3%endmatrix* 
& \
%cline2-6
hhline~~----
& 3 
& beginmatrix*[r] 98.6% \ -42.7% \ 95.7% \ 94.2%endmatrix* 
& cellcolorblack!12 
 beginmatrix*[r] phantom-99.9% \ 73.4% \ 99.1% \ 99.3%endmatrix* 
& beginmatrix*[r] phantom-199.9% \ -40.1% \ 99.3% \ 96.7%endmatrix* 
& beginmatrix*[r] phantom-99.7% \ 72.8% \ 99.4% \ 98%endmatrix* \
cline2-6
& 4 
& beginmatrix*[r] 0.0% \ phantom-67.8% \ 93.2% \ 93.0%endmatrix* 
& beginmatrix*[r] 99.5% \ -23.5% \ 95.4% \ 93.0%endmatrix* 
& beginmatrix*[r] phantom-199.9% \ 73.9% \ 5.3% \ 93.0%endmatrix* 
& beginmatrix*[r] 99.9% \ 74% \ -87.1% \ 96.5%endmatrix* \
cline2-6
& 5 
& beginmatrix*[r] -99.7% \ -82.9% \ -99.4% \ 93.0%endmatrix* 
& beginmatrix*[r] -99.8% \ 64.9% \ 2.7% \ 93.0%endmatrix* 
& beginmatrix*[r] -100.5% \ -69.8% \ 59.1% \ 93.0%endmatrix* 
& beginmatrix*[r] -0.4% \ 73.9% \ 14.4% \ phantom-93.1%endmatrix* \
hline
endarray
]
enddocument